Adapting to Climate Change: a Risk Assessment And

Adapting to climate change: A risk assessment and decision making framework for managing groundwater dependent ecosystems with declining water levels Supporting Document 3: Identifying thresholds for responses of amphibians to groundwater and rainfall decline

Nicola Mitchell, Bea Sommer and Peter Speldewinde

Adapting to climate change: A risk assessment and decision making framework for managing groundwater dependent ecosystems with declining water levels

SUPPORTING DOCUMENT 3: Identifying thresholds for responses of amphibians to groundwater and rainfall decline

The University of Western Australia

Authors

Nicola Mitchell – The University of Western Australia Bea Sommer – Edith Cowan University Peter Speldewinde – The University of Western Australia Published by the National Climate Change Adaptation Research Facility 2013 ISBN: 978-1-925039-37-5 NCCARF Publication 66/13

Australian copyright law applies. For permission to reproduce any part of this document, please approach the authors.

Please cite this report as: Mitchell, N, Sommer, B & Speldewinde, P 2013, Adapting to climate change: A risk assessment and decision making framework for managing groundwater dependent ecosystems with declining water levels. Supporting document 3: Identifying thresholds for responses of amphibians to groundwater and rainfall decline, National Climate Change Adaptation Research Facility, Gold Coast, 33 pp.

Acknowledgement This work was carried out with financial support from the Australian Government (through the Department of Climate Change and Energy Efficiency and the National Water Commission) and the National Climate Change Adaptation Research Facility (NCCARF). The role of NCCARF is to lead the research community in a national interdisciplinary effort to generate the information needed by decision-makers in government, business and in vulnerable sectors and communities to manage the risk of climate change impacts.

Disclaimer The views expressed herein are not necessarily the views of the Commonwealth or NCCARF, and neither the Commonwealth nor NCCARF accept responsibility for information or advice contained herein.

Cover image: A male crawling frog, Pseudophryne guentheri calling from a terrestrial nest in Lake Pinjar on the Gnangara mound, Western Australia © Dr Nicola Mitchell, the University of Western Australia, School of Animal Biology TABLE OF CONTENTS

ABSTRACT ...... 1 EXECUTIVE SUMMARY...... 2 1. INTRODUCTION ...... 3 2. METHODS ...... 4 2.1 Study location and species dataset ...... 4 2.2 Multivariate analysis of species abundance related to environmental drivers ... 6 2.3 Use of expert opinion to define thresholds ...... 7 2.4 Worked examples of scenarios ...... 8 3. RESULTS ...... 11 3.1 Overview ...... 11 3.2 Is the spatio-temporal distribution of amphibian assemblages related to habitat characteristics? ...... 11 3.2.1 Trapping data ...... 11 3.2.2 Aural data ...... 14 3.3 Bayesian Belief Networks developed by expert opinion ...... 17 3.3.1 Aquatic-breeding guild ...... 17 3.3.2 Terrestrial-aquatic breeding guild ...... 21 3.3.3 Terrestrial breeding guild ...... 25 4. DISCUSSION ...... 27 5. CONCLUSION ...... 30 REFERENCES ...... 31

Identifying thresholds for responses of amphibians to groundwater and rainfall decline i LIST OF FIGURES

Figure 1. Amphibian species occurring in the study area, arranged by breeding guild .. 5 Figure 2. Locations of frog aural survey sites in the ‘short-term’ gnangara sustainability strategy project, in addition to other locations where data were available on frogs ...... 7 Figure 3. Life history diagram for the crawling frog, showing key nodes (in blue) incorporated in to the bbn as thresholds for population responses in the terrestrial- aquatic breeding guild...... 9 Figure 4. Pcoa ordination showing the trapping data coded by season (autumn or winter) with sites coded into season, overlain with frog species...... 11 Figure 5. Cap plot for spring trapping data of 32 sites covering the timeframe 2003- 2011 with sites colour-coded by basin moisture ...... 12 Figure 6. Pcoa plot coded by lithology overlain with amphibian species...... 12 Figure 7. Dbrda of spring trapping data coded by lithology...... 13 Figure 8. Pcoa ordination showing trajectory of change in the amphibian assemblage detected from spring trapping surveys for the lexia epp173 site from 2003-2009...... 13 Figure 9. Cap plot for spring and autumn aural survey data of 122 sites covering the timeframe 1999-2011 with sites colour-coded by lithology ...... 15 Figure 10. Pco sites from the aural surveys of amphibians, coded into season...... 16 Figure 11. Dbrda of the spring aural surveys, with sites coded by year...... 16 Figure 12. Pcoa ordination showing trajectory of change in the amphibian assemblage detected from spring aural surveys for the site epp173 from 2003-2009...... 17 Figure 13. Bbn for aquatic breeding amphibians, illustrating the impact of groundwater between 1-2 m from the surface, a 2-3 month hydroperiod, and a decline in the winter breeding trigger ...... 18 Figure 14. The influence of groundwater and the hydroperiod on the probability of population persistence for the quacking frog ...... 19 Figure 15. The influence of groundwater and the hydroperiod on the probability of population persistence for the squelching frog ...... 19 Figure 16. The influence of groundwater and the hydroperiod on the probability of population persistence for the rattling froglet ...... 20 Figure 17. The influence of groundwater and the hydroperiod on the probability of population persistence for the western banjo frog ...... 20 Figure 18. The influence of groundwater and the hydroperiod on the probability of population persistence for the motorbike frog and the slender tree frog ...... 21 Figure 19. A bbn for terrestrial-breeding amphibians with aquatic larvae, illustrating the impact of groundwater between 1-2 m from the surface, a hydroperiod less than three month, and a decline in the autumn breeding trigger ...... 22 Figure 20. The relationship between groundwater levels and probability of ‘extreme decline’ for the crawling frog, illustrating the influence the hydroperiods and seasonal rainfall triggers for key events in the species’ lifecycle...... 23 ii Identifying thresholds for responses of amphibians to groundwater and rainfall decline Figure 21. The relationship between groundwater levels and probability of ‘extreme decline’ for the moaning frog, illustrating the influence of the hydroperiod and seasonal rainfall triggers for key events in the lifecycle ...... 24 Figure 22. A simple bbn for the turtle frog - a terrestrial-breeding amphibian ...... 25 Figure 23. The relationship between groundwater levels and probability of population persistence for the turtle frog, illustrating the influence of seasonal rainfall triggers for key events in the lifecycle...... 26

LIST OF TABLES

Table 1. Summary of amphibian survey sites and sampling periods on the gnangara mound ...... 6 Table 2. List of experts providing input in to the bbns ...... 9

Table 3. Life history* of the amphibian species on the gnangara mound ...... 10

Identifying thresholds for responses of amphibians to groundwater and rainfall decline iii iv Identifying thresholds for responses of amphibians to groundwater and rainfall decline ABSTRACT

Amphibians are key indicators of wetland health and under conditions of hydrological change it is important to be able to predict changes in their diversity and abundance. Here we develop a methodology for predicting how nine amphibian species with different life histories could potentially respond to declining groundwater, and declining rainfall – both of which are occurring on the Gnangara Mound north of Perth in south- western Australia. This example can be considered as ‘data-poor’ because although we had access to data on amphibian assemblages and relative abundance from systematic surveys, we could derive few insights into the environmental drivers of such patterns using multivariate analysis. Instead we turned to amphibian biologists with relevant expertise on Gnangara Mound amphibians to derive conceptual models of the most important factors explaining whether populations would persist or decline under anticipated environmental change. These models were constructed as Bayesian Belief Networks (BBNs) and were developed for each of three reproductive guilds: amphibians that breed in water, amphibians that breed in terrestrial nests that are later flooded, and one entirely terrestrial-breeding species. The models showed that aquatic breeding species were most sensitive to changes in the hydroperiods, but were unable to demonstrate an impact of groundwater level because we lacked the information to derive an empirical link between groundwater and hydroperiods. The terrestrial-aquatic breeding species were also sensitive to hydroperiod length, with declines in autumn and winter rainfall further decreasing the probabilities of population persistence. The BBN developed for the Turtle frog – the terrestrial-breeding species – assumed that groundwater levels would influence soil moisture and that this species would experience population declines if groundwater levels were either high or very low. Hence, situations where groundwater-dependent wetlands transition to terrestrial ecosystems under groundwater decline could potentially suit Turtle frogs provided that an appropriate vegetation community develops. While the BBNs developed here are largely conceptual, and thus preliminary, they demonstrate a promising approach for anticipating the impacts of groundwater decline on amphibians, provided that the links between hydrological processes and amphibian thresholds can be determined empirically or mechanistically. Our models also demonstrate the key role that seasonal rainfall events play in triggering reproduction, and suggest that the drier climates projected for south-western Australia will place additional stress on amphibian communities.

Identifying thresholds for responses of amphibians to groundwater and rainfall decline 1 EXECUTIVE SUMMARY

In this project we developed Bayesian Belief Networks (BBNs) that described the responses of each of three reproductive guilds of amphibians to groundwater decline and weather variables. While the distribution of amphibian species occurring within our study region (the Gnangara mound) had been systematically surveyed for a previous project since 1999, the dataset was not well suited to multivariate analysis of the environmental drivers that explained presence or absence at breeding sites. These analyses were designed to feed into the ‘effects assessment’ and ‘risk characterization’ components of the risk assessment process. Although spatial patterns were evident in the data, particularly with regard to species assemblages on the Bassendean and Spearwood soil complexes, multivariate regression tree (MRT) analyses designed to identify hydrological (and other) thresholds could not be applied because the data did not meet the requirements for this type of analysis, particularly in relation to number of observations and the relatively short time frame over which the data were collected. Similarly, there was an absence of empirical data on environmental tolerance thresholds of embryonic, larval and adult life stages for the nine species currently occurring on the Gnangara mound.

In this ‘data poor’ situation we used the opinions of four experts on amphibian biology to derive separate BBNs for three groups of amphibians based on differences in their reproductive modes. The first group consisted of six species that deposit eggs in water (the Myobatrachid frogs Crinia glauerti, C. georgiana, C. insignifera and Limnodynastes dorsalsis, and the Hylid species Litoria adelaidensis and Litoria moorei). The second group consisted of two species with terrestrial embryos and aquatic larva (Heleiporus eyrei and Pseudophryne guentheri), and a final network was constructed for a terrestrial species that breeds underground (the turtle frog Myobatrachus gouldii). In all cases, a reduction in seasonal rainfalls that trigger breeding activity (or other key events such as flooding of nest sites) were viewed as important drivers of population declines. Similarly, a reduction in the hydroperiod (potentially due to declining groundwater, reduced rainfall or alteration to the catchment) and water quality (due to salinization) was considered to jeopardise recruitment to metamorphosis.

In a previous study of amphibians on the Gnangara Mound, five species (H. eyrei, C. georgiana, L. dorsalis, L. adelaidensis and L. moorei) were considered to be reasonably robust to hydrological decline due to either their longevity or because they favoured large water bodies with capacity for contraction. In contrast, three species (C. glauerti, C. insignifera and P. guentheri) were viewed as being sensitive to hydrological change due to their relatively short life cycles and specific breeding requirements. We tested whether our networks captured these different expectations of species vulnerability by driving our BBNs with similar thresholds and filters, and examining probabilities of population persistence or decline. We found that the terrestrial-aquatic breeding group were the most vulnerable to population decline, with the P. guentheri being more vulnerable than H. eyrei, in keeping with the earlier assessment. All aquatic breeding frogs were predicted to persist unless the hydroperiod was less than a critical threshold (determined by expert opinion) that would allow time for each species to reach metamorphosis. The probability of persistence of the turtle frog (a fossorial species) was sensitive to groundwater levels, and depended on intermediate groundwater levels that moderated suitable soil moisture at the underground retreat sites and nest sites of this species. This species could potentially benefit from hydrological change if former wetlands become terrestrial ecosystems, but turtle frogs depend on functioning Banksia woodlands which are vulnerable to over-abstraction of groundwater.

2 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 1. INTRODUCTION

Amphibians are highly susceptible to any process that threatens the quality and periodicity of wetland habitats (Bradford 2002; Bunnell and Ciraolo 2010). Breeding sites are diverse, and include seepages, watercourses, floodplains or wetlands, and in some regions these water bodies are groundwater-dependent. While most species of amphibians utilise aquatic breeding sites, many species have terrestrial embryos that develop in nest sites adjacent to water bodies. Embryos are subsequently flooded when the water table rises following seasonal rainfall, triggering hatching. The initiation of breeding activity in terrestrial-breeding species is critically dependent on moist soils that prevent the dehydration of males calling from nest sites, and that are wet enough to prevent the desiccation of eggs that develop in the nest (Andrewartha et al. 2008; Mitchell 2001; 2002). Hence, the wetting of surface soils at the break of season is a key driver of breeding events in terrestrial-breeding amphibians.

Typically, soil wetting is a top-down process that is dependent on rainfall, but groundwater levels and vegetation dynamics can also affect soil moisture profiles, and hence the distance to groundwater can potentially moderate the suitability of breeding sites of amphibians that nest in underground burrows. For example, the Western Australian Turtle frog, Myobatrachus gouldii is a species with direct developing eggs that are deposited up to 1.5 m underground in sandy soils (Roberts 1981). This species depends on moderately wet soils, as waterlogged soils dramatically reduce the ambient oxygen available for the developing embryos. Hence this species tends to occupy terrestrial habitats that are not subject to groundwater intrusion (Bamford 1992) and could potentially benefit from groundwater decline as wetlands transition to terrestrial ecosystems.

Abstraction of groundwater for domestic and industrial purposes has led to the decline of amphibian populations in other regions of the world, notably in North America (Bradford 2002; Bunnell and Ciraolo 2010). This is largely because decreasing groundwater connectivity has led to declining hydroperiods in ephemeral water bodies, or has led to the transition of permanent water bodies to ephemeral systems. This in turn affects the capacity of amphibian species to complete the larval (tadpole) phase of the lifecycle, with premature drying of water bodies leading to failed recruitment. Declining rainfall, and shifts in the seasonality of rainfall is an additional stressor to amphibian populations, not only because rainfall recharges groundwater, but because these events often trigger reproduction (Walls et al. 2013). Regions of south-western Australia are currently faced with both groundwater decline and rainfall decline (Refer to Section 3.1.1 of the Development and Case Studies document), and the purpose of this technical report is to develop a methodology for assessing how environmental variables such as groundwater, hydroperiods and rainfall influence population trends in amphibians, and to apply the methodology using future groundwater and climate scenarios.

Identifying thresholds for responses of amphibians to groundwater and rainfall decline 3 2. METHODS

2.1 Study location and species dataset

The amphibian case study developed for this project was based on the species assemblage occurring on the Gnangara Mound. Details of the study location and climate are described in Section 3.1 of the Development and Case Studies Report (Chambers et al. 2013). Thirteen species of amphibians have been recorded on the Gnangara Mound, of which four are occasional vagrants that have not been recorded in recent decades (Bamford and Huang 2009). The nine species that currently occur on the mound fall into three broadly defined breeding guilds: six species that have aquatic embryos and larvae (tadpoles), two species with terrestrial embryos and aquatic larvae, and a single fossorial species that breeds in Banksia woodlands (Figure 1). This latter species, the Turtle frog (Myobatrachus gouldii) has direct-developing eggs that develop 0.8 -1.5 m underground and hatch as fully formed frogs. This breeding strategy is highly unusual, but is shared by two other western Australian amphibians (the northern and southern sandhill frog, Arenophryne rotunda and Arenophryne xiphorhyncha; Doughty and Edwards 2008).

Nationally, very few long-term datasets exist on the diversity and distributions of amphibians in groundwater dependent wetlands. However, due to concern about the impacts of groundwater abstraction on the biota of the Gnangara Mound, the Western Australian Department of Water (formerly Water and Rivers Commission) commissioned the monitoring of amphibians across this region in 1999, and monitoring has continued under various initiatives up until 2011. This monitoring data was compiled and made available to the current project by Bamford Consulting Ecologists. The data consisted of estimates of the abundance of each species from aural surveys (listening for calling males and night during the autumn and spring during the typical breeding seasons), and was initially conducted by staff from the Department of Terrestrial Vertebrates at the Museum of Western Australia (Aplin et al. 2001). In 2002, the project was transferred to Bamford Consulting Ecologists (Davis and Bamford 2004). Following the 2002 survey, changes were implemented so that the project focussed more intensely on a smaller number of wetlands than was the case in the original study, and this approach was used annually from 2003 to 2009. In 2008, additional aural survey sites were included in the program as part of the Gnangara Sustainability Strategy (GSS) project with 59 sites located across the Gnangara Mound (Bamford and Huang 2009). In 2010 and 2011, additional pitfall trapping sites were added to the program as it was considered important to examine the recruitment success of a representative species (in this case, the terrestrial-breeding Moaning Frog, Heleioporus eyrei) as a measure of the impact of changes in groundwater levels. Two of the nine species were not adequately surveyed across the Gnangara Mound: the motorbike frog which calls in late spring and summer and hence was detected rarely in the aural surveys conducted in early spring, and the turtle frog, which calls on only a few nights each year (Mitchell 2011) and was only detected in the trapping surveys. This species was also trapped extensively during the GSS project, but these data were not sought for this study. A summary of data types and sources is shown in Table 1 and their distribution across the Gnangara Mound is shown in Figure 2.

4 Identifying thresholds for responses of amphibians to groundwater and rainfall decline Turtle frog Moaning frog Crawling frog Myobatrachus gouldii Heleioporus eyrei Pseudophryne guentheri

Quacking frog Rattling froglet Squelching froglet Crinia georgiana Crinia glauerti Crinia insignifera

Western banjo frog Limnodynastes dorsalis Motorbike frog Slender tree frog Litoria moorei Litoria adelaidensis

Figure 1. Amphibian species occurring in the study area, arranged by breeding guild (red = terrestrial; purple = terrestrial-aquatic; blue = aquatic). The motorbike frog are slender tree frog are in the Family Hylidae, while the remaining species are all ground frogs in the family Myobatrachidae. All photographs by Nicola Mitchell, except Limnodynastes dorsalis (Mike Brown) and Crinia glauerti (Evan Pickett).

Two of the nine species were not adequately surveyed across the Gnangara Mound: the motorbike frog which calls in late spring and summer and hence was detected rarely in the aural surveys conducted in early spring, and the turtle frog, which calls on only a few nights each year (Mitchell 2011) and was only detected in the trapping surveys. This species was also trapped extensively during the GSS project, but these data were not sought for this study. A summary of data types and sources is shown in Table 1 and their distribution across the Gnangara Mound is shown in Figure 2.

Identifying thresholds for responses of amphibians to groundwater and rainfall decline 5 Table 1. Summary of amphibian survey sites and sampling periods on the Gnangara Mound

Monitoring East Lexia GSS GSS Whiteman Series Wetlands short term long term Park

Number of sites 6592018 Date initiated 1999 2008 2010 2007 Date of last data 2011 2010 2011 2007 Survey type Aural and trapping (2 Aural Aural and Aural sites) trapping (4 sites)

The vegetation and hydrological changes at two trapping sites that had the largest amounts of data (East Lexia Wetland sites LEX86 and EPP173) are described below.

LEX86 (31°45’13’’S, 115°57’29’’E) LEX86 contains dense Baumea articulata and Typha orientalis stands and a riparian fringe of large Melaleuca trees. In 2003, the wetland basin was dry in May but the wetland was extensively flooded in October. In 2004, the wetland basin was damp in May but almost dry by October. Water levels were higher in 2005, with the wetland flooded in both early June and October/November. In 2006, the wetland did not flood but contained temporary pools in late winter. The failure of this wetland to contain water in 2006 was due to very poor winter rainfall. In 2007 and 2008, Lexia 86 wetland was dry in June and October. It was damp with pools in May 2009 but was dry by October of the same year

EPP173 (31°42’19’’S, 115°57’45’’E) This wetland is largely undisturbed and heavily vegetated with dense stand of Baumea articulata and Typha species, emergent shrubs and a dense riparian fringe of Melaleuca and other species. The wetland appears to be permanent and flows into adjacent paddocks when water levels are high. Water levels peak in spring and in some years (2004 and 2005) the wetland overflows into adjacent paddocks and there is extensive flooding of riparian vegetation. In 2003, 2006, 2007, 2008 and 2009, however, the overflow did not occur and flooding of the riparian vegetation was limited.

2.2 Multivariate analysis of species abundance related to environmental drivers

While our amphibian dataset was not species rich in comparison to datasets for aquatic macroinvertebrates and wetland vegetation (SD2 Sommer et al. 2013), there was considerable overlap in the monitoring sites and years over which these three datasets were collected. We therefore attempted to define thresholds that defined each species’ response to groundwater and other environmental variables using an identical process to that described for the Gnangara Mound macroinvertebrates and vegetation (SD2 Sommer et al. 2013). Any thresholds identified that related to groundwater levels could then be incorporated in to a Bayesian Belief Network (BBN) and potentially analysed on a GIS platform.

6 Identifying thresholds for responses of amphibians to groundwater and rainfall decline All amphibian datasets were split into ‘trapping’ and ‘aural’ datasets, and then in to spring and autumn observation periods. Aural abundance categories (e.g. 1-10, 11-30, >30, >100) were converted to absolute values (5, 22, 35 and 120 respectively) and sites that had missing data (e.g. not sampled in some years, or where no species were detected) were excluded. Amphibian data were log (x+1) transformed before PCoA and db-RDA were carried out using the Primer Permanova v. 6 software package (SD2 Sommer et al. 2012).

Figure 2. Locations of frog aural survey sites in the ‘short-term’ Gnangara Sustainability Strategy project (red circles with site codes), in addition to other locations where data were available on frogs. Figure from Bamford and Huang 2009 (Copyright the Government of Western Australia, the Department of Environment and Coservation).

2.3 Use of expert opinion to define thresholds

Given the limited insights we ultimately derived from the multivariate analysis, we turned to using expert opinion to decide on the thresholds and structure of our BBNs, as is often necessary in data poor situations (Hosack, Hays, and Dambacher, 2008). One of the important features of BBNs is that the probabilities do not need to be exact to be useful. BBN’s are generally robust to imperfect knowledge and approximate probabilities (even educated guesses) very often give very good results. Expert opinion has several roles in BBN networks (Cain, 2001): 1) the development of the model structure, including the identification of nodes and linkages between nodes, 2) the population of conditional probability tables for nodes, and 3) review of BBN models.

Identifying thresholds for responses of amphibians to groundwater and rainfall decline 7 In the example reported here, we took the approach of dividing the nine amphibian species currently occurring in the GSS into three functional groups: 1) frogs requiring permanent water, 2) frogs with terrestrial embryos and aquatic larvae, and 3) the entirely terrestrial Turtle Frog. This approach had the advantage of producing fewer BBNs than had we had produced networks for individual species, but allowed us to compare how each functional ‘group’ responded to declining rainfall and groundwater levels. For each group, a conceptual model was first derived by one expert (Mitchell) indicating how major environmental variables influenced the survival of these species.

A half-day workshop was then convened with experts on Gnangara Mound frogs. Six local scientists were invited to participate in the workshop, and four accepted. All four participating experts had doctoral degrees in herpetology and recent experience working on amphibians in the Gnangara study system, and the experts included one of the scientists who collected data provided by Bamford Consulting ecologists (Table 2). Experts were first asked if they agreed with the conceptual models and given the opportunity to modify the models, on the proviso that the preference was for a simple model over a more complex one. Once agreement on model structure was reached, expert opinion was then used to populate the conditional probability tables of the BBN. This process consisted of showing the group the model and then working through each node in the model and allowing experts to discuss their opinions on the probability of outcomes before reaching a consensus. This method was chosen given that the expert panel was small (four people) and the models were not overly complex (five nodes in the case of the Turtle Frog model). Once conditional probability tables for each node were completed, experts were given the opportunity to alter the tables if required and simple scenarios were run through the model to check if model outcomes matched with the expected outcome predicted by the expert panel. In general, experts relied on a combination of their knowledge of relevant life history publications, unpublished data, and personal experience to decide on the structure of the conceptual model and the probability values. For completeness, a table of life history parameters and relevant sources of data are included in Table 3, but note that this information was not provided to the expert panel.

2.4 Worked examples of scenarios

We ran a complete range of scenarios for each BBN, with a focus on presenting the interactions between the groundwater node and other parent nodes in the model (usually hydroperiods and seasonal rainfall nodes). A detailed description of the nodes in each BBN are included in SD6 (Speldewinde 2013), along with a sensitivity analysis relating to groundwater levels.

8 Identifying thresholds for responses of amphibians to groundwater and rainfall decline Figure 3. Life history diagram for the Crawling frog, showing key nodes (in blue) incorporated in to the BBN as thresholds for population responses in the terrestrial-aquatic breeding guild.

Table 2. List of experts providing input in to the BBNs

Expert Institution Relevant background Professor J Dale School of Animal Conducted research and published Roberts Biology, University widely on Western Australian of Western Australia amphibians since 1978. Familiar with the Gnangara study area.

Dr Nicola Mitchell School of Animal Conducted research on terrestrial- Biology, University breeding amphibians in the Gnangara of Western Australia study area since 2005, and published widely on terrestrial-breeding species.

Dr Leonie Valentine School of Plant Worked for the Gnangara Sustainability Biology, University Strategy Taskforce since 2008; survey of Western Australia work included trapping amphibians in the Gnangara study area.

Dr Wes Bancroft Bamford Consulting Works for the consultants who Ecologists produced the 2009 report ‘The occurrence and status of frogs in the Gnangara Sustainability Strategy study area’ and generated some of the amphibian datasets.

Identifying thresholds for responses of amphibians to groundwater and rainfall decline 9 Table 3. Life history* of the amphibian species on the Gnangara mound

Common name and Scientific name Relevant life history information Embryonic Larval Require References reproductive guild lifespan (d) lifespan flooding? (d) Terrestrial Direct-developing fossorial species. Emerge to feed after rainfall Turtle frog Myobatrachus gouldii (primarily in winter) and for late spring/early summer courtship. 60 n/a No Roberts 1981, Mate 0.8- 1.5m underground at the end of summer. Eggs hatch Mitchell 2011 and metamorphs emerge after the break of season in autumn. Terrestrial-aquatic

Pseudophryne guentheri Terrestrial breeding species with breeding peak in late May once Crawling frog soils wet up after autumn rainfall. Embryos can survive long 40-60 60 Yes Main 1965; periods on land, but flooding of nest sites is required to trigger Eads et al. 2012 hatching and larval development

Terrestrial breeding species with breeding peak in April/May; Moaning frog Heleioporus eyrei males begin calling before break of season and travel large 30 150 Yes Bamford 1992, distances to wetlands. Foam nests deposited at the base of Lee 1967, Main burrows up to 0.5 m deep. Flooding of burrows required to trigger 1965 hatching and larval development. Aquatic Breed in winter, typically in shallow seepages. Eggs deposited in Quacking frog Crinia georgiana depressions and larvae washed out following rainfalls 5 30-45 n/a Main 1965, Seymour & Roberts 1995 Breed from May-July, typically in shallow water in ephemeral Squelching froglet Crinia insignifera wetlands or at the margins of permanent wetlands 2 Up to 150 n/a Main 1957, 1968 Breeds from July -October, typically in swamps and streams. Rattling froglet Crinia glauerti 3 100 n/a Main 1965, 1968, Littlejohn 1959 Breed in winter and early spring, foam nests deposited amongst Western Banjo frog Limnodynastes dorsalis vegetation in permanent water 3 4 n/a Main 1965, Martin 1972 Breed in winter and spring, eggs typically attached to submerged Slender tree frog Litoria adelaidensis vegetation in permanent water 3 100 n/a Main 1965 Breed in late spring and summer, typically in permanent water Motorbike frog Litoria moorei 3 120-365 n/a Main 1965

* Additional information on habitat types and historical prevalence on the Gnangara Mound can be found in Bamford and Huang (2009).

10 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 3. RESULTS

3.1 Overview

Because the multivariate analyses were not satisfactory in terms of identifying practical hydrological (and other) thresholds, and thereby assessing risk, the Bayesian Belief networks we ultimately developed were based on expert opinion. For completeness, we present the basic multivariate analyses below in Section 3.2, and present more detailed outputs from the BBNs developed using expert opinion in Section 3.3.

3.2 Is the spatio-temporal distribution of amphibian assemblages related to habitat characteristics?

3.2.1 Trapping data All nine of the amphibian species known to currently occur on the Gnangara Mound were trapped from at least one of the two survey sites at the East Lexia Wetlands (LEX86 and ESS173). A principal coordinate analysis (PCoA) of all trapping datacoded by the survey period (Autumn or Spring) shows the seasonal distribution of observations (Figure 4. As the spring trapping data tended to be more species rich (Bamford and Huang 2009) we restricted the remainder of our analyses to the spring dataset only. A canonical analysis of Principal Coordinates (CAP) showed a weak association between the composition of amphibian species trapped at each site in spring and the basin moisture classification (Figure 5), whereas other habitat variables could not be analysed using CAP due to only having two categories. Instead, a PCoA of the spring data coded by lithology is presented (Figure 6) but a PCoA coded into vegetation groups is not shown as there were only two groups (most wetlands had trees/shrubs/sedges and rushes, while two wetlands, 36-11s and 5-10 had only tree and shrubs).

Season 40 Autumn Spring

EPP173-09sEPP173-07s EPP173-07a

20 LEX86-09s EPP173-05a EPP173-05sEPP173-04a 36-11s EPP173-06s LEX86-04aLEX86-06sLEX86-08s EPP173-08sLEX86-07aEPP173-03s EPP173-09a Crinia glauerti LEX86-08a EPP173-04s EPP173-08aEPP173-06aLEX86-06a Crinia georgiana 0 LEX86-04s EPP173-03a44-11s LEX86-03sLEX86-09a LEX86-07s Myobatrachus gouldi 25a-10s

PCO2 (17.3 % of total variation) LEX86-05sLEX86-03a Limnodynastes dorsalis Heleioporus eyrei -20 LEX86-05a Crinia insignifera

Pseudophryne guentheri Litoria adelaidensis 5-10s -40

-60 -40 -20 0 20 40 60 PCO1 (48.9% of total variation)

Figure 4. PCoA ordination showing the trapping data coded by season (autumn or winter) with sites coded into season, overlain with frog species.

Identifying thresholds for responses of amphibians to groundwater and rainfall decline 11 Basin Moisture

0.2 Dry Not Recorded LEX86-09s Limited Flooding LEX86-08aLEX86-08s Wet/Damp Overflow Flooding LEX86-04aLEX86-06s EPP173-07s

0.1 EPP173- LEX86-04s 36-11s EPP173-03s EPP173-04a 25a-10s Myobatrachus gouldii EPP173- LEX86-07s EPP173-06aLEX86-06a CAP2 EPP173-04s 0 LEX86-07a EPP173-05a Litoria adelaidensis Crinia georgianaEPP173-06s LEX86-05a Crinia glauerti EPP173-09s Limnodynastes dorsalis Crinia insignifera EPP173-08s EPP173-05s LEX86-03sLEX86-09a5-10s Pseudophryne guentheri 44-11sHeleioporus eyrei -0.1 LEX86-03a EPP173-09a

EPP173-03a

LEX86-05s

-0.2 -0.2 - 0 0.1 0.2 0.3 CAP1 Figure 5. CAP plot for spring trapping data of 32 sites covering the timeframe 2003-2011 with sites colour-coded by basin moisture. Squared canonical correlations were CAP1 = 0.51 and CAP2 = 0.24. The two canonical test statistics were significant (P = 0.024 and 0.034 respectively, using 999 permutations). Species overlain in blue show which species tended to be associated with each site but show no convincing patterns with regard to the basin moisture classifications.

Lithology 40 Bassendean Transition

EPP173-09s EPP173-07s

20 LEX86-09s 36-11s LEX86-06s LEX86-08s EPP173-05s EPP173-03s EPP173-06sEPP173-08s LEX86-04s 0 EPP173-04s LEX86-03s LEX86-07s Crinia glauerti 44-11s Myobatrachus gouldi 25a-10s LEX86-05s Crinia georgiana PCO2 of (28.8% variation) -20

LimnodynastesHeleioporus dumerilieyrei Crinia insignifera

Pseudophryne guentheri -40 5-10s Litoria adelaidensis

-60 -40 -20 0 20 40 PCO1 (36.8% of total variation) Figure 6. PCoA plot coded by lithology overlain with amphibian species.

12 Identifying thresholds for responses of amphibians to groundwater and rainfall decline A distance-based redundancy analysis (dbRDA) showed that only rainfall (pseudo-F 2.21, P< 0.05) and mean minimum temperature (pseudo-F 2.26, P< 0.05) significantly explained the distribution of observations (Figure 7).

Lithology Bassendean LEX86-05s Transition EPP173-03sEPP173-05s 20

EPP173-06s 5-10s

EPP173-04s 25a-10s LEX86-04s LEX86-07sEPP173-09s 0 LEX86-03s Date of 44-11sPeak to peak Depth to staff gauge (m) TotalLEX86-09s rainfall (mL) EPP173-08s 36-11s EPP173-07s dbRDA2 (34.1% of of 15.6% fitted, variation) total Mean min temperatureLEX86-08s Trough to -20 Mean global solar exposure (winter) LEX86-06s

Mean max temperature

-40 -20 0 20 40 dbRDA1 (37.7% of fitted, 17.3% of total

Figure 7. dbRDA of spring trapping data coded by lithology.

PCO2 (28.5% of total variation) 20

EPP173-09s

EPP173-08s 10 EPP173-06s

PCO2 of (28.5% variation) EPP173-05s EPP173-04s

-10 EPP173-07s

EPP173-

-20 -30 -20 -10 0 10 20 30 PCO1 (48.1% of total variation) Figure 8. PCoA ordination showing trajectory of change in the amphibian assemblage detected from spring trapping surveys for the Lexia EPP173 site from 2003-2009.

Identifying thresholds for responses of amphibians to groundwater and rainfall decline 13 A (PCoA) was used to show a trajectory of change for the Lexia wetland site EPP173. In 2003, 2006, 2007, 2008 and 2009 the flooding of riparian vegetation was limited, whereas vegetation was flooded in 2004 and 2005. 3.2.2 Aural data Eight of the nine amphibian species were detected from the aural surveys, but one of these eight - the Motorbike frog – was considered to have been inadequately surveyed as the timing of the surveys did not coincide with the peak in the breeding season (Bamford and Huang 2009). The undetected species was the Turtle frog, which only calls on a few nights each year, usually in late spring and summer (Mitchell 2011).

In spite of significant test statistics, the CAP analysis showed no clear associations between frog species aural data and lithology (Figure 9). This is in contrast to the littoral vegetation and macroinvertebrates on the Gnangara mound which showed very strong associations (SD2 Sommer et al. 2013). However, there was clear separation between spring and autumn surveys, a reflection of the fact that most species call in spring (Figure 10). A dbRDA analysis showed that of the environmental drivers tested, only the mean maximum and the mean minimum winter/spring temperature (pseudo-F 4.52 and 5.49 respectively, both P< 0.01) and the solar exposure in winter (pseudo-F 2.92, P< 0.05) significantly explained the distribution of the observations from the aural surveys (Figure 11). The dbRDA further shows that the 2010 observations (all to the left of the x-axis) were particularly associated with higher winter/spring minimum temperatures. The PCoA in Figure 12 shows that there appears to be a directional change in species composition at EPP173, particularly from 2004 onwards. What exactly this change constitutes would have to be investigated in more detail, however it appears the site was experiencing higher numbers of L. adelaidensis, C. glauerti and C. insignifera (based on calls) towards 2011.

14 Identifying thresholds for responses of amphibians to groundwater and rainfall decline Lithology 0.05 Bassendean Spearwood Transition G4609sG4410sLY08sLY10sLY09s LY11sLY07sG4611s LY05a LY06a Mel7308s G0611a G3610s G0511sG0611sG0411s G4311aG0311a EPP08sG4711sG4610s PL8709sEPP06sG4110sG4109s G4911sG4910sG4710sEPP03sEPP05sG4909sG4709sG4409sL8609sEPP04sLY06sG3609s G4111s G4610a G0309sG3611s G4511s G4411sEPP07sEPP11s G2509s L8604a G4410aL8605s L8603s L18607aG4110a Mel7307s CAP 2 0 G0311s L8607aL9407aG2110aL9408a G30a11aMel7308aG4010aG3611aG2511aG4810aG4211aG4511aG4811aMel7810aG3610aG0711aMel7811aL18610aEPP11aL18611aEPP09aG4011aL8609aG3010aG2910aG2510aG0511aG2411aG2911aG3011aL9411aLY09aLY10a EPP08a G4911a L8606aG0410aG0710aG0310aL18605aL8610aL9404aL8611aL8605aL9410aEPP10a G0610aG0510aL9405a EPP04a Mel7305sG0609s L8608aL18604a G30a11s G4411aEPP05aEPP06a LY05s G25a11sG4710aG4611aG4711aG4910a G4111aLY07a

-0.05 -0.10 -0.05 0 0.05 0.10 CAP1

Figure 9. CAP plot for spring and autumn aural survey data of 122 sites covering the timeframe 1999-2011 with sites colour-coded by lithology. Squared canonical correlations were CAP1 = 0.18 and CAP2 = 0.13. The two canonical test statistics were significant (both P = 0.004, using 999 permutations), and overall 60% of sites were correctly allocated. Most misclassifications occurred for the Transition group (20% correct, versus 72.8% classified correctly for the Bassendean group and 56% classified correctly for the Spearwood group).

Identifying thresholds for responses of amphibians to groundwater and rainfall decline 15 80 Season Autumn Spring G2110aL8607aL9407a L8608a L9408a 60

L18607a

Pseudophryne guentheri G30a11 s 40 L18604a L8605a EPP04 LY07a L9405a a G0311s G0610aG0510a L8604a Crinia insignifera L8606aL9404a Lymnodynastes dorsalis G0410a Crinia georgiana L18605a Mel7305sG0609sLY05s EPP08a 20 G0710aG0310a EPP06a Littoria mooreiCrinia glauerti L8610a EPP05a G25a11sL8605sMel7307s G4910aG4710aG4611aG4711a Heleioporus eyrei G0309s G3611s L8611a G4411a L9410a G4111a G0411sG0611sG0511sG0711sEPP11sL8603sG4511sG4411sEPP07s EPP10a Litoria adelaidensisG4111s 0 G4410a G2509s G4911aMel7308s PCO2 of (14.5% variation) G4610a EPP08sLY06sEPP03sEPP05sG4911sG4910s G4710sEPP06sG4610sG4711sG3609s LY06aLY05a G4709sG4909sG4110sG4409sG4109sEPP04sL8609s L8609aG3010aG2910aG2510aG0511aG2411aG2911aG3011aLY09aLY10aL9411a G4110a PL8709sG3610s Mel7308aMel7810aG30a11aL18610aL18611aMel7811aG4011aG3610aG0711aEPP09aEPP11aG4010aG4810aG3611aG2511aG4511aG4811aG4211a LY11s G4611sLY07s -20 G4410sLY09sG4609sLY10sLY08s

G0311aG4311a G0611a -40 -60 -40 -20 0 20 40 60 PCO1 (50.3% of total variation) Figure 10. PCO sites from the aural surveys of amphibians, coded into season.

40 Year 2003 G4410s 2004 EPP11s 2005 LY10s 2006 G4910s G4511s 2007 G4110s 2008 20 G4909s G4411s 2009 G4611sG4711s 2010 Trough to peak solarG4609sG4709s exposure (WINTER) 2011 L8609s G4911s G4610sG4710s Date of peak/trough G4109sPL8709s LY11s G3610sMean MAX winter/spring temp G0309sG0609sG4111s LY08s G4409s 0 Mean MIN winter/spring temp G30a11sG3609s LY09s G0311sG0411sG0511sG0611sG0711s LY07s DepthMel7308sEPP08sLY06s G3611s EPP04s L8603sMel7307sEPP07s G25a11s G2509sEPP06s LY05s dbRDA2 dbRDA2 of fitted, (23.19% of total 10.3% variation) L8605s Peak to peak -20 EPP03s winter/spring rainfall Mel7305sEPP05s

-40 -40 -20 0 20 40 dbRDA1 (60.9% of fitted, 19.6% of total variation) Figure 11. dbRDA of the spring aural surveys, with sites coded by year.

16 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 40

Crinia georgiana

EPP11s 20 EPP08s Litoria adelaidensis Crinia glauerti Crinia insignifera

EPP03sEPP05s 0

EPP07s PCO2 (45.6% of variation)

EPP04s -20 EPP06s

-40 -40 -20 0 20 40 PCO1 (59.3% of total variation) Figure 12. PCoA ordination showing trajectory of change in the amphibian assemblage detected from spring aural surveys for the site EPP173 from 2003- 2009.

3.3 Bayesian Belief Networks developed by expert opinion

3.3.1 Aquatic-breeding guild The amphibian experts concurred that a key driver of population persistence for the six species in the aquatic reproductive guild was the hydroperiod of the wetland (or other waterbody), as this parameter is critical for larvae having sufficient time to complete metamorphosis and to disperse from wetlands. While hydroperiods are almost certainly dependent on groundwater in many wetlands on the Gnangara Mound, we had no means of deriving an empirical link between groundwater level and surface water expression. Hence, hydroperiod was set as an independent node with defined monthly increments (see SD6; Speldewinde 2013). Groundwater level did contribute to the network through a salinity node, as there was empirical data relating groundwater levels to electrical conductivity for each lithology class in the GSS (see SD2 Sommers et al. 2012), and evidence from other Australian species of amphibian that salinity above a threshold of 8ppt leads to high levels of deformity and morbidity in tadpoles (e.g. Kearney et al. 2012). However, based on this empirical data, the probability of salinity above the 8ppt threshold were always very small.

The four tadpole survival filters estimated the probabilities of ‘extreme decline’, ‘slight decline’ or ‘persist’ under different combinations of salinity and hydroperiod. The species that required a minimum 1-month hydroperiod (the Quacking frog) was influenced by Tadpole survival 1, whereas species requiring a minimum 2, 3 and 4- month hydroperiod were influenced by Tadpole survival 2,3 and 4 respectively.

17 Identifying thresholds for responses of amphibians to groundwater and rainfall decline Lithology Ground_water_level Hydroperiod Spearwood 50.0 greater than 0 0 less than one mnth 0 Bassendean and transition 50.0 zero to neg1 0 one to two mnths 0 neg1 to neg2 100 two to three mnths 100 neg2 to neg3 0 three to four mnths 0 neg3 to neg4 0 more than four mnths 0 less than neg4 0 Winter_breeding_trigger winter present 0 winter decline 100

Salinity less than 8ppt 97.5 more than 8ppt 2.50

Tadpole_survival_1 Tadpole_survival_2 Tadpole_survival_3 Tadpole_survival_4 no 2.50 no 7.38 no 95.1 no 100 yes 97.5 yes 92.6 yes 4.88 yes 0

Quacking_frog Squelching_froglet Rattling_froglet Extreme decline 2.50 Extreme decline 7.38 Extreme decline 95.1 Slight decline 29.3 Slight decline 9.26 Slight decline 0 Persist 68.3 Persist 83.4 Persist 4.88

Western_banjo_frog Slender_tree_frog Extreme decline 100 Extreme decline 100 Slight decline 0 Slight decline 0 Persist 0 Persist 0

Motorbike_frog Extreme decline 100 Slight decline 0 Persist 0

Figure 13. BBN for aquatic breeding amphibians, illustrating the impact of groundwater between 1-2 m from the surface, a 2-3 month hydroperiod, and a decline in the winter breeding trigger.

18 Identifying thresholds for responses of amphibians to groundwater and rainfall decline Hydroperiod 0-20 20-40 40-60 Hydroperiod 0-20 20-40 40-60 4.5 4.5 (mo.) (mo.) 3.5 3.5 2.5 100 2.5 100 1.5 80 1.5 80 0.5 0.5 60 60 40 40 20 20 a) 0 b) 0 Probability of persistence persistence of Probability persistence of Probability

-4.5 -3.5 -4.5 -3.5 -2.5 -1.5 -2.5 -1.5 -0.5 0.5 -0.5 0.5 Groundwater level relative to surface (m) Groundwater level relative to surface (m)

Figure 14. The influence of groundwater and the hydroperiod on the probability of population persistence for the Quacking frog, with a) the winter-breeding trigger present, or b) in decline.

a) b)

Figure 15. The influence of groundwater and the hydroperiod on the probability of population persistence for the Squelching frog, with a) the winter-breeding trigger present, or b) in decline.

Three of the six aquatic breeding amphibians were viewed as requiring a winter rainfall trigger to initiate breeding, hence the BBN was structured to cause a reduction in the probability of population persistence under a scenario of winter rainfall decline. Figures 14, 15 and 17 show examples of scenarios run with and without a decline in winter rainfall, but in general, the influence of this node was very small (see sensitivity analysis in SD6; Speldewinde 2013).

The probabilities of persistence for the remaining three species (Figures 16 and 18) were influenced primarily by the hydroperiod node, with very little influence from the groundwater node that modified salinity according to the underlying lithology. The direct influence of the lithology parent node was not examined as a sensitivity analysis (Table 11; SD6; Speldewinde et al.) showed that this node was relatively unimportant. This was because empirical data showed that the probability of salinity increase was very low, and therefore lithology (which impacts on salinity) was inconsequential.

19 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 0Ͳ20 20Ͳ40 40Ͳ60 60Ͳ80 80Ͳ100 4.5 Hydroperiod 3.5 (mo.) 2.5 100 1.5 80 0.5 60

0 of persistance Probability

-4.5 -3.5 -2.5 -1.5 -0.5 0.5 Groundwater level relative to surface (m)

Figure 16. The influence of groundwater and the hydroperiod on the probability of population persistence for the Rattling froglet. This species breeds opportunistically after rainfall, except during summer months.

a) b)

Figure 17. The influence of groundwater and the hydroperiod on the probability of population persistence for the Western Banjo frog, with a) the winter-breeding trigger present, or b) in decline.

20 Identifying thresholds for responses of amphibians to groundwater and rainfall decline Figure 18. The influence of groundwater and the hydroperiod on the probability of population persistence for the Motorbike frog and the Slender tree frog. These species were both influenced by the same tadpole survival node in the BBN, and hence their probabilities of persistence were identical. 3.3.2 Terrestrial-aquatic breeding guild Only two species were incorporated in to the BBN for the terrestrial-aquatic breeding guild, and although these species were both autumn breeders they depended to different extents on seasonal rainfalls to initiate breeding (Figure 19). The Moaning frog - a larger, species than the Crawling frog that burrows deeper underground, can begin calling before the break in season, but peak breeding occurs at the break of season. In contrast, the Crawling frog begins calling at the break of season but peak breeding is delayed for several weeks as the shallow surface soils where nests are constructed increase in water content. The BBN was structured to reflect this link between autumn rain and soil moisture, where it was assumed that a decline in autumn rainfall would result in sub optimal soil moisture for reproductive activity (Figure 19). Unpublished data on the crawling frog conducted during a record dry year in 2006 (N. Mitchell) supports this relationship. The expert panel introduced a second rainfall node to denote winter rainfall, which prevents the cue for hatching when nest sites flood (Bradford and Seymour 1985).

Like the BBN for the aquatic breeding guild, the aquatic larvae of these species depend on a suitable hydroperiod to allow metamorphosis, and are vulnerable to salinity (Davis and Roberts 2011). The relationships between the Lithology, Ground water level and Salinity nodes were therefore constructed from the same empirical data as was used in the BBN for the aquatic-breeding amphibians. Similarly, a tadpole survival filter was constructed by estimating the probabilities of extreme decline, slight decline and persistence under different combinations of salinity and hydroperiod. An analysis of the interrelationships between groundwater levels, the hydroperiod, and the presence of decline of seasonal rainfall is shown for each species in Figures 20 and 21.

21 Identifying thresholds for responses of amphibians to groundwater and rainfall decline Ground_water_level greater than 0 0 Lithology zero to neg1 0 Spearwood 50.0 neg1 to neg2 100 Bassendean and transition 50.0 neg2 to neg3 0 neg3 to neg4 0 less than neg4 0

Salinity less than 8ppt 97.5 Hydroperiod more than 8ppt 2.50 less than 3 mnths 100 more than 3 mnths 0

Winter_hatching_trigger Autumn_rainfall winter rainfall present 100 autumn present 0 winter rainfall decline 0 autumn decline 100

Tadpole_survival Soil_moisture no 80.5 low 100 yes 19.5 high 0

Crawling_frog Moaning_frog Extreme decline 85.4 Extreme decline 40.3 Slight decline 4.87 Slight decline 50.0 Persist 9.75 Persist 9.75

Figure 19. A BBN for terrestrial-breeding amphibians with aquatic larvae, illustrating the impact of groundwater between 1-2 m from the surface, a hydroperiod less than three month, and a decline in the autumn breeding trigger. The difference in dependence on the autumn rainfall trigger is primarily driving the different responses between the two species.

22 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 100 HP > 3 months, autumn rainfall present, winter hatching trigger present

90 HP > 3 months, autumn rainfall decline, winter hatching trigger present

80 HP > 3 months, autumn rainfall present, winter hatching trigger decline HP > 3 months, autumn rainfall decline, winter hatching trigger decline 70 HP < 3 months, autumn rainfall present, winter hatching trigger present 60 HP < 3 months, autumn rainfall decline, winter hatching trigger present

50 HP < 3 months, autumn rainfall present, winter hatching trigger decline

HP < 3 months, autumn rainfall decline, winter hatching trigger decline 40

30 Probabbility of extreme decline of decline extreme Probabbility

0 Ͳ5 Ͳ4 Ͳ3 Ͳ2 Ͳ1 0 1

Groundwater level relative to surface (m)

Figure 20. The relationship between groundwater levels and probability of ‘extreme decline’ for the Crawling frog, illustrating the influence the hydroperiods and seasonal rainfall triggers for key events in the species’ lifecycle.

23 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 100 HP > 3 months, autumn rainfall present, winter hatching trigger present

90 HP > 3 months, autumn rainfall decline, winter hatching trigger present

50 HP < 3 months, autumn rainfall present, winter hatching trigger decline

HP < 3 months, autumn rainfall decline, winter hatching trigger decline 40

30 Probabbility of extreme decline Probabbility

0 Ͳ5 Ͳ4 Ͳ3 Ͳ2 Ͳ1 0 1

Groundwater level relative to surface (m)

Figure 21. The relationship between groundwater levels and probability of ‘extreme decline’ for the Moaning frog, illustrating the influence of the hydroperiod and seasonal rainfall triggers for key events in the lifecycle

24 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 3.3.3 Terrestrial breeding guild The single terrestrial-breeding species (the Turtle frog) was included in this case study as an interesting example of a species whose probability of persistence could potentially increase with groundwater decline. The relationship between groundwater level and population density is unknown for this species, but anecdotal evidence suggests that the species favours slightly elevated areas that are presumably more distant from the water table. Although soil moisture values at the underground retreat and breeding sites of this species have been measured (N. Mitchell, unpublished data) the influence of groundwater depth on soil moisture has not been determined in this habitat (primarily Banksia woodland), and is undoubtedly complex. Hence a conceptual link was developed between a groundwater node and a soil moisture node (Figure 22), the latter of which had three levels, with the ‘medium’ soil moisture being best suited to embryonic survival (dry soils would lead to embryonic desiccation, whereas wet soils would cause embryonic death due to hypoxia). It was assumed that the optimum ‘medium’ soil moisture conditions would be experienced when groundwater was relatively distant from the soil surface.

As for the other amphibian BBNs, two seasonal rainfall events were viewed as being important for population persistence: spring rainfall that promotes courtship at the soil surface (Roberts 1981; Mitchell 2011) and autumn rainfall that provides the trigger for the emergence of metamorphs from nest sites up to 1.5 m underground (Roberts 1981). The influence of groundwater level, and potential declines in these seasonal rainfall triggers is shown in Figure 23).

Ground_water_level greater than 0 0 zero to neg1 0 neg1 to neg2 0 neg2 to neg3 0 neg3 to neg4 100 less than neg4 0

Spring_rainfall_trigger Autumn_rainfall_trigger spring present 100 autumn present 0 spring decline 0 autumn decline 100

Soil_moisture low 10.0 medium 90.0 high 0

Turtle_frog Extreme decline 10.0 Slight decline 27.0 Persist 63.0

Figure 22. A simple BBN for the Turtle frog - a terrestrial-breeding amphibian

25 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 100

90 Spring and autumn rainfall trigger present

80 Spring rainfall trigger present, autumn trigger decline Spring rainfall trigger decline, autumn trigger present 70 Spring rainfall trigger decline, autumn trigger decline 60

20 Probabbility ofpopulation persistance

0 Ͳ5 Ͳ4 Ͳ3 Ͳ2 Ͳ1 0 1

Groundwater level relative to surface (m)

Figure 23. The relationship between groundwater levels and probability of population persistence for the Turtle frog, illustrating the influence of seasonal rainfall triggers for key events in the lifecycle.

26 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 4. DISCUSSION

The influence of the groundwater node in two of the three BBNs developed for amphibians was negligible (Figures 14-18, 20-21). The sole influence of the changes in the groundwater level were mediated via the salinity node, and the range of groundwater levels that we modelled never predicted the critical salinity threshold of 8ppt and therefore did not influence any of the output nodes. Instead, the hydroperiod had the most appreciable influence on the probability of population persistence of these two guilds, as the expert panel had constructed the BBNs with a tadpole survival filter that reflected the combined influence of wetland hydroperiods and salinity.

Hydroperiod thresholds were based on best guesses of minimum larval lifespans. Further refinement of the larval lifespans of each species could increase the utility of the BBNs, but such basic life-history data is often unknown. Furthermore, temperature has an appreciate influence on embryonic and larval development rates (e.g. Mitchell 2000) and under a climate change scenario of warmer water temperatures, larval lifespans would be correspondingly shorter. Therefore quantification of the larval lifespans for the various species at current environmental temperatures would be valuable for accurately populating the thresholds for tadpole survival.

The apparent negligible influence of groundwater levels on amphibian species that require water to complete their lifecycle is unlikely to be realistic. The hydroperiod of any wetland or water body that is groundwater dependent will be directly affected by groundwater decline, but in this instance we lacked the empirical data from the multivariate analyses to link groundwater levels to hydroperiods. However, monitoring by the Western Australian Department of Water has shown a clear reduction in the expression of surface water (and therefore hydroperiods) associated with groundwater declines on the Gnangara Mound (Sonneman 2009), and terrestrial-aquatic breeding amphibians that breed in the sumplands have experienced several years of failed recruitment (N. Mitchell, unpublished observations).

To demonstrate a link between hydroperiods and groundwater levels in our BBNs we could have devised a hypothetical relationship (i.e. higher groundwater levels producing longer hydroperiods), but the disadvantage of this approach is that it would be misleading for perched or artificial water bodies. That is, amphibians could persist in perched wetlands provided that the hydroperiod is sufficient to allow recruitment of juveniles in to the population. An alternative approach to demonstrating a realistic relationship between groundwater levels and hydroperiods would be to use a hydrological model to predict hydroperiods from groundwater, rainfall, soil type/porosity and catchment inputs (e.g. Colletti et al. 2012). Modelled predictions can then be spatially explicit and driven by GIS (e.g. Mitchell at al. 2013), but modelled hydroperiods were well beyond the scope and timeframe of this study.

Aside from the wetland hydroperiod, the other nodes most influencing population persistence were declines in seasonal rainfall. Record low rainfalls in autumn and winter have been experienced in the south west of Australia in the past decade, and the trend is likely to continue (Bureau of Meteorology, 2012; Indian Ocean Climate Initiative 2012), hence seasonal rainfall declines pose a very real threat to the reproductive success of amphibians. For example, during a period of record low autumn rainfall in 2006, recruitment of the Crawling frog at a site on the Darling Escarpment failed, due to the combined effect of desiccation of embryos and failure of nest sites to flood (N. Mitchell, unpublished data). More subtle effects of desiccation stress have also been recorded in this species, including slower hatching times, smaller body sizes, increases asymmetry and reduced hatching success (Eads et al.

27 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 2012). Notwithstanding these effects, declines in seasonal rainfall will also directly reduce hydroperiods. Our BBNs could have been constructed to reflect such a dependency between nodes, but to improve tractability we limited the influence of declines in seasonal rainfall to their effects on triggering key events in amphibian lifecycles.

Overall, our BBNs suggested that the terrestrial-aquatic breeding amphibians had the highest probabilities of ‘extreme decline’ under the various constructs of the network (Figures 20 and 21). One of these species – the Crawling frog – was also viewed in a related study to be the species most vulnerable to population decline, partially due to its short lifespan and specific habitat requirements (Bamford and Huang 2009). Conversely, the other terrestrial-aquatic breeder was considered by the same authors to be reasonability robust to hydrological change, due to its longevity and high dispersal ability (Bamford 1991). This highlights one of the inadequacies of the existing BBNs, in that they do not account for differences in longevity, reproductive output or dispersal. While experts may have intuitively made allowances for such species’ differences when populating the various conditional probability tables, these considerations are not tractable.

The BBN developed for the terrestrial breeding turtle frog (Figure 22) was the only model that demonstrated how changes in groundwater level could directly modify the probability of persistence (Figure 23). In this case, the groundwater level node controlled the soil moisture node. Sensitivity analysis of the Turtle frog BBN shows no entropy reduction when the groundwater depth is either < 1 m of higher (i.e. soil is saturated or flooded) or below 4m. At these depths the soil moisture is entirely unsuitable for the Turtle Frog and therefore the rainfall nodes become irrelevant in the model. In between these two extremes, soil moisture (and by inference groundwater level) was a highly relevant influence on the output node. Hence the predictions of the impact of declining groundwater at a wetland for a turtle frog would be an increasing probability of population persistence. There would, however, be a significant time lag before this could occur, as turtle frogs inhabit mature Banksia stands and feed on the associated invertebrate community (primarily termites). Because Banksia species could take decades to colonise and transform former wetland habitats it is unrealistic to assume that turtle frogs would replace other amphibian species in drying wetlands in the short term.

Seasonal rainfall triggers also modified the probabilities of population persistence for the Turtle frog, with a decline in the autumn rainfall trigger having a slightly greater influence than a decline in the spring rainfall trigger (Figure 23). This is because the experts viewed the rainfall trigger that initiates courtship as being fairly flexible in its timing (courtship behaviours have been recorded between September and February in this species; Roberts 1981). In contrast, a decline in autumn rainfall would lead the later emergence (and hence later opportunities for feeding) of metamorphs, which could potentially lead to reduced survival.

A key groundwater-dependent process that is likely to be highly influential in the persistence of turtle frogs on the Gnangara Mound is the health of the Banksia Woodlands. Over-abstraction of groundwater has led to the death of Banksia stands at long-term study sites (Groom et al. 2000) and recovery of these woodlands after groundwater recharge is slow. Again, there may be a time lag between the decline of a Banksia woodland and the associated turtle frog population, because termite abundance may remain high in dead trees. However, the impact of living Banksias on hydrological processes such as regulation of soil moisture is potentially profound. Largely due to uncertainties in the relationships between groundwater levels, Banksia health and soil moisture, a Banksia Health node was not incorporated into the BBN.

28 Identifying thresholds for responses of amphibians to groundwater and rainfall decline With improved understanding (and potentially modelling) of these interactions, a more complex BBN could be developed to investigate the response of this unique amphibian to hydrological change.

29 Identifying thresholds for responses of amphibians to groundwater and rainfall decline 5. CONCLUSION

In data-poor situations such as the amphibian example developed here, we have demonstrated that Bayesian Belief networks constructed using expert opinion can provide insights into the responses to groundwater decline in a diverse range of species. Further, we demonstrate how weather variables that are important to recruitment can be incorporated into BBNs. In situations where parent nodes such as rainfall and groundwater levels could be projected in a spatially explicit manner, BBNs constructed using expert opinion can be used with greater utility. For example, they could be applied to particular wetlands where high-resolution data on depths to the water table are available, where hydroperiods can be modelled or derived empirically, and where future climate change scenarios have been projected at an appropriate scale. In this way, managers could anticipate the impact of groundwater abstraction at significant wetlands, and initiate appropriate responses to enhance the probability of the persistence of the amphibian community and the associated ecosystem services they convey.

30 Identifying thresholds for responses of amphibians to groundwater and rainfall decline REFERENCES

ANDREWARTHA, S. J., MITCHELL, N. J. & FRAPPELL, P. B. 2008. Phenotypic differences in terrestrial frog embryos: effect of water potential and phase. Journal of Experimental Biology, 211, 3800-3807.

APLIN K, MARYAN B, PERFUMO J, and KIRKPATRICK P. 2001. East Lexia Frog Monitoring: Winter – Spring 2001. Dept. Terrestrial Vertebrates, WA Museum and Ecosystems Environmental Consultants. Unpublished Report to the Water and Rivers Commission.

BAMFORD, M. J. 1992. The impact of fire and increasing time after fire upon Heleioprus eyrei, Limnodynastes dorsalis and Myobatrachus gouldii (Anura: Leptodactylidae) in Banksia woodland near Perth, Western Australia. Wildlife Research, 19, 169-178.

BAMFORD, M. J. & HUANG, N. 2009. The occurrence and status of frogs in the Gnangara Sustainability Strategy study area. Report prepared on behalf of the Department of Environment and Conservation for the Gnangara Sustainability Strategy Area.

BRADFORD, D.F. 2002. Amphibian Declines and Environmental Change in the Eastern Mojave Desert. Conference Proceedings. Spring-fed Wetlands: Important Scientific and Cultural Resources of the Intermountain Region, p 1-7. http://www.wetlands.dri.edu

BRADFORD, D. F. & SEYMOUR, R. S. 1985. Energy conservation during the delayed- hatching period in the frog Pseudophryne bibroni. Physiological Zoology, 58, 491-496.

BUNNELL, J. F. & CIRAOLO, J. L. 2010. The potential impact of simulated groundwater withdrawals on the oviposition, larval development, and metamorphosis of pond-breeding frogs. Wetlands ecology and management, 18, 495-509.

BUREAU OF METEOROLOGY. 2012. http://www.bom.gov.au/social/2012/08/driest- july-for-southwest-western-australia/ Accessed 19 December 2012

CAIN, J. 2001 Planning improvements in natural resources management - guidelines for using Bayesian networks to support the planning and management of development programmes in the water sector and beyond. Unpublished report. Centre for Ecology and Hydrology, Oxford, UK

CANHAM, C., FROEND, R., STOCK, W. 2009. Water stress vulnerability of four Banksia species in contrasting ecohydrological habitats on the Gnangara Mound, Western Australia. Plant Cell and Environment, 32, 64-72

CHAMBERS, J., NUGENT, G., SOMMER, B., SPELDEWINDE, P., NEVILLE, S., BEATTY, S., CHILCOTT, S., EBERHARD, S., MITCHELL, N., D’SOUZA, F., BARRON, O., MCFARLANE, D., BRAIMBRIDGE, M., ROBSON, B., CLOSE, P., MORGAN, D., PINDER, A., FROEND, R., HORWITZ, P., COOK, B. and DAVIES, P. 2013. Development and case studies - Adapting to climate change: a risk assessment and decision making framework for managing groundwater dependent ecosystems with declining water levels, National Climate Change Adaptation Research Facility, Canberra, Australia.

31 Identifying thresholds for responses of amphibians to groundwater and rainfall decline COLETTI, J. Z., HINZ, C., VOGWILL, R. & HIPSEY, M. R. 2012. Hydrological controls on carbon metabolism in wetlands. Ecological Modelling, (in press).

DAVIS, R. & BAMFORD, M. 2004. Report on East Lexia Frog Monitoring. Autumn/Spring 2003. Unpublished report to Water and Rivers Commission, Perth.

DAVIS, R. A. & ROBERTS, J. D. 2011. Survival and Population Size of the Frog Heleioporus albopunctatus in a Highly Modified, Agricultural Landscape. Copeia, 2011, 423-429.

DOUGHTY, P. & EDWARDS, D. L. 2008. A new species of sandhill frog (Myobatrachidae: Arenophryne) from the western coast of Australia. Records of the Western Australian Museum 24, 121-131.

EADS, A., MITCHELL, N. J. & EVANS, J. 2012. Patterns of genetic variation in desiccation tolerance in embryos of the terrestrial-breeding frog, Pseudophryne guentheri. Evolution, 66, 2865-2877.

GROOM, P. K., FROEND, R. H. & MATTISKE, E. M. 2000. Impact of groundwater abstraction on a Banksia woodland, Swan Coastal Plain, Western Australia. Ecological Management & Restoration, 1, 117-124.

HOSACK, G. R., HAYS, K. R. & DAMBACHER, J. M. 2008. Assessing model structure and uncertainly through an analysis of system feedback and Bayesian networks. Ecological Applications 18, 1080-1082.

INDIAN OCEAN CLIMATE INITIATIVE, 2012. www.ioci.org.au/ Accessed 19 December 2012

KEARNEY, B. D., BYRNE, P. G. & REINA, R. D. 2012. Larval Tolerance to Salinity in Three Species of Australian Anuran: An Indication of Saline Specialisation in Litoria aurea. PloS one, 7, e43427.

KUHNERT, P. M., MARTIN, T. G. & GRIFFITHS, S. P. A guide to eliciting and using expert knowledge in Bayesian ecological models. 2010. Ecology Letters, 13, 900-914.

LITTLEJOHN, M. J. 1959. Call differentiation in a complex of seven species of Crinia (Anura: Leptodactylidae). Evolution, 13, 452-468.

MAIN, A. R. 1957. Studies in Australian amphibia. I. The genus Crinia Tschudi in south-western Australia and some species from south-eastern Australia. Australian Journal of Zoology, 5, 30-55.

MAIN, A. R. 1968. Ecology, systematics and evolution of Australian frogs. Advances in Ecological Research, 5, 37-86.

MAIN, A. R. 1965. Frogs of southern western Australia, Perth, Western Australian Naturalists' Club.

MARTIN, A. A. 1972. Studies in Australian Amphibia III. The Limnodynastes dorsalis complex (Anura: Leptodactylidae). Australian Journal of Zoology, 20, 165-211.

32 Identifying thresholds for responses of amphibians to groundwater and rainfall decline MITCHELL, N. J. & SEYMOUR, R. S. 2000. Effects of temperature on the energy cost and timing of embryonic and larval development of the terrestrially breeding moss frog, Bryobatrachus nimbus. Physiological and Biochemical Zoology, 73, 829-840.

MITCHELL, N. J. 2001. Males call more from wetter nests: effects of substrate water potential on reproductive behaviours of terrestrial toadlets. Proceedings B of the Royal Society of London, 268, 87-93.

MITCHELL, N. J. 2002. Low tolerance of embryonic desiccation in the terrestrial nesting frog Bryobatrachus nimbus (Anura: Myobatrachinae). Copeia, 2002, 364-373.

MITCHELL, N. J. 2011. Turtle frogs: bizarre breeders of the Banksia woodland. In Perth's Banksia Woodlands, precious and under threat, Urban Bushland Council of Western Australia, Perth, Western Australia, p 47-49.

MITCHELL, N., HIPSEY, M. R., ARNALL, S., MCGRATH, G., BIN TAREQUE, H., KUCHLING, G., VOGWILL, R., SIVAPALAN, M., PORTER, W.P. & KEARNEY, M.R. 2013. Linking Eco-Energetics and Eco-Hydrology to Select Sites for the Assisted Colonization of Australia’s Rarest Reptile. Biology, 2, 1-25.

ROBERTS, J. D. 1981. Terrestrial breeding in the Australian leptodactylid frog Myobatrachus gouldii (Gray). Australian Wildlife Research, 8, 451-462.

SEYMOUR, R. S. & ROBERTS, J. D. 1995. Oxygen uptake by the aquatic eggs of the Australian frog Crinia georgiana. Physiological Zoology, 68, 206-222.

SOMMER, B., MCGUINNESS, S., FROEND, R. & HORWITZ, P. 2013. Assessing risks to groundwater dependent wetland ecosystems in a drying climate: an approach to facilitate adaptation to climate change. Supporting document 2 for the NCCARF project - Adapting to climate change: a risk assessment and decision framework for managing groundwater dependent ecosystems with declining water levels, National Climate Change Adaptation Research Facility, Canberra, Australia.

SONNEMAN, T. 2009. Lake Pinjar Vegetation Assessment and Ecological Linkages. A report to the Gnangara Sustainability Strategy. Department of Environment and Conservation, Perth, Australia.

SPELDEWINDE, P. 2013. Development of Bayesian Belief Networks for modeling the impacts of falling groundwater due to climate change on groundwater dependent ecosystems. Supporting document 6 for the NCCARF project - Adapting to climate change: a risk assessment and decision framework for managing groundwater dependent ecosystems with declining water levels, National Climate Change Adaptation Research Facility, Canberra, Australia.

WALLS, S.C., BARICHIVICH, W.J. & BROWN, M.E. 2013. Drought, deluge and declines: the impact of precipitation extremes on amphibians in a changing climate. Biology, 2, 399-418.

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