Drivers of Spatial and Temporal Movement Patterns of Acanthopagrus Butcheri Through an Estuarine Surge Barrier

Drivers of spatial and temporal movement patterns of Acanthopagrus butcheri through an estuarine surge barrier

Submitted by Richelle McCormack

This thesis is presented for the degree of Bachelor of Science Honours. College of Science, Health, Engineering and Education, Murdoch University

2019

Declaration

I declare this thesis is my own account of my research and contains as its main content work which has not been previously submitted for a degree at any tertiary education

institution.

Richelle McCormack

Acknowledgements

I would like to extend a very special thank you to all my supervisors. Dr Stephen

Beatty for all his expertise and knowledge on freshwater ecosystems and statistics; Dr James Tweedley for his expert knowledge on the Vasse-Wonnerup Estuary and thorough editing of all my work; and Dr Alan Cottingham for his expert knowledge on all things Black Bream, south-west Australian estuaries and for teaching me the ropes on catch and release and PIT tagging of fish in the middle of the night on board a little rickety dinghy in Busselton. I feel so lucky to have had three amazing academics by my side throughout my Honours experience, who have worked collaboratively to make this as much an enjoyable and educational experience as Honours can be. They all dedicated so much time and effort in covering my drafts in red ink and meeting with me for countless hours, and I am so grateful for their dedication.

My supervisors also introduced me to a wealth of professionals who aided in my research. Thank you to Tom Ryan for his technical assistance and initial set up of the PIT antenna system. I extend a lot of gratitude to GeoCatch and Department of Water and Environmental Regulation (DWER) and the Water Corporation for the hydrological data and Bureau of Meteorology (BoM) for the environmental data without which this project would not have been possible. The fieldwork components of this project were also funded by DWER (IRMA 17379) with support from GeoCatch, so another massive thanks for that. My sincere gratitude goes to Karl Pomorin Karltek whose technology in conjunction with the PIT system made tracking fish from the comfort of my lounge room possible. Thank you to the Busselton and Molloy Senior high schools for assisting in the collection of in situ data, and the wider Busselton community for showing a genuine interest in the health and management of the Vasse-Wonnerup Estuary. The study was conducted under Murdoch University Animal Ethics Committee permit RW2793/15 and Department of Primary Industries and Regional Development (Fisheries) Exemption

2902. I acknowledge the Noongar people who are the Traditional Custodians of the land on which my research took place.

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To the great friends I’ve made through the last year and a half that have provided moral support, motivation and just great banter- Elysia Tingey and Georgina Stagg, it’s been comforting knowing we’ve all been in the same boat, so thank you so much! Last but definitely not least, a huge thank you and deepest appreciation and love to my incredible partner Tyson Addicoat who has supported me in every way throughout this project. His emotional support, positivity and ability to put up with my sleep deprivation and stress induced moods in particular has been nothing short of heroic. To all my friends and family that I have had to cancel plans on and have not seen for a while, thank you for your understanding, and I cannot wait to make up for lost time in seeing you all now that my studies are complete... until next time!

Abstract Coastal and estuarine environments are popular sites for human settlement, yet they are among the most vulnerable to changing climate and extreme weather events such as rising sea level and storm surges. Storm surge barriers have been installed in numerous estuaries around the world to mitigate flooding risk. However, these structures have numerous deleterious impacts on ecological connectivity by restricting flow and fragmenting habitats, thus preventing fishes from accessing preferred spawning, nursery and feeding areas. Despite the ecological impact of estuarine surge barriers being well recognised, few studies have investigated their impact on obligate estuarine fishes; particularly at the individual level.

The highly degraded Vasse-Wonnerup Estuary in south-western Australia has suffered regular mass fish kills, and fish gates were installed on the storm surge barriers to enable two-way fish passage in times of poor water quality. However, the majority of recent fish kills have occurred immediately upstream of the Vasse Surge Barrier (VSB) suggesting the gates have been ineffective in facilitating movement. The sparid Acanthopagrus butcheri has been particularly impacted by these fish kills. Due to its large body size, life-history characteristics and socio-economic importance in southern Australia, this obligate estuarine species is ideal to investigate how fish passage through the VSB may be influenced by prevailing environmental conditions.

The fine-scale movement patterns of passive integrated transponder (PIT) tagged A. butcheri were monitored through the VSB using a custom designed system between 20th March 2017 and 31st May 2018. Passage data were analysed together with a suite of hydrological and environmental variables using generalised additive mixed models to determine the drivers of fish approaches (i.e. those detected at the downstream site of the fish gate without subsequently passing through) and the daily and hourly upstream and downstream passages through the fish gate.

Daily approaches of A. butcheri to the VSB were typically greatest during September-December and April-May. As the species is known to spawn in July-October in the system, the increase in PIT detections in spring may have been partially associated v with an adult upstream migration. However, the key spawning site for the species is known to occur in another region of the system (i.e. the ‘Deadwater’ region) rather than habitats upstream of the VSB. This fact, along with the increase in detections at the VSB that occurred during April-May outside of the spawning period, suggests that the peaks in detections at the VSB may have been attributed to high localised migration, rather than representing spawning activity.

Hourly upstream and downstream passages through the fish gate were nocturnal and crepuscular, respectively. Downstream passages were also associated with declines in dissolved oxygen concentrations in the upstream habitats; suggesting that A. butcheri was seeking to escape poor water quality. However, the hourly and daily upstream and downstream passages of A. butcheri were also strongly associated with times of minimal flow velocity within the fish gate that occurred when water levels equalised on the upstream and downstream sides of the VSB. Therefore, while the species appeared to be avoiding poor water quality by passing through the fish gate, it appeared this could only occur during certain hydrological conditions. This likely limited its ability to freely escape from times of poor water quality, thus explaining the periodic fish kills that occur mostly upstream of the VSB.

These findings have clear implications for the management of the VSB and also instream barriers in other systems that house A. butcheri. A key recommendation for the future management of the VSB is to automate the fish gate operation so it opens during times of upstream and downstream water equalisation. This would maximise fish passage opportunities and simultaneously prevent salt-water intrusion upstream prevents stratification and associated hypoxia and toxic algal blooms.

Given the projected increase in sea level rise and decrease in rainfall in south- western Australia, and indeed many parts of the world, associated with climate change, the construction of storm surge barriers is becoming more prevalent. This study highlights the need to understand the movement patterns and life-history requirements of resident estuarine species to maintain connectivity to critical habitats.

Contents

Acknowledgements ...... iii

Abstract ...... v

1. Introduction ...... 1 1.1. Estuaries and their fish faunas ...... 1 1.2. Threats to estuaries ...... 3 1.3. Instream barriers ...... 5 1.4. South-western Australian estuaries ...... 7 1.5. Acanthopagrus butcheri...... 8 1.6. Aims and hypotheses ...... 9

2. Materials and Methods ...... 10 2.1. Study site...... 10 2.2. Surge barrier and fish fauna ...... 13 2.3. Sampling regime ...... 17 2.3.1. Environmental variables ...... 19 2.3.2 Hydrological conditions of fish passage ...... 20 2.4. Statistical analyses ...... 21 2.4.1. Generalised additive mixed models...... 21

3. Results ...... 25 3.1. Environmental variables ...... 25 3.2. Factors influencing approaches to the Vasse Surge Barrier ...... 29 3.3. Hydrological conditions of fish passage ...... 32 3.4. Factors influencing daily downstream and upstream passage through the Vasse Surge Barrier fish gate ...... 32 3.5. Factors influencing the hourly downstream and upstream passage through the Vasse Surge Barrier fish gate ...... 38

4. Discussion ...... 40 4.1. Factors influencing the approaches of Acanthopagrus butcheri to the Vasse Surge Barrier ...... 40 4.2. Factors influencing the passage of Acanthopagrus butcheri through the Vasse Surge Barrier ...... 42 4.3. Study limitations and future research ...... 44 4.4. Management implications and recommendations ...... 46 4.5. Conclusion ...... 47

5. References ...... 49

6. Appendices ...... 60

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1. Introduction

1.1. Estuaries and their fish faunas

Estuaries are situated at the interface of terrestrial, marine and freshwater realms, facilitating the exchange of tidal and fresh water, organic matter and nutrients (Howarth et al., 1991; Tweedley et al., 2016). These systems comprise a diverse suite of physico-chemical environments each of which typically exhibit rapid nutrient cycling and biological production (Hoellin et al., 2013). Thus, it is unsurprising that estuaries are among the most productive of all aquatic ecosystems and therefore have great ecological importance including providing rich fisheries and feeding areas for migrating shore birds (Schelske and Odum, 1962; Kennish, 2003; Hoellin et al., 2013; Sheaves et al., 2014; Tweedley et al., 2016). The varied geomorphological and physico-chemical characteristics of estuaries (Lam-Hoai et al., 2006; Elliott and Quintino, 2007; Dauvin and Ruellet, 2009) has resulted in many definitions being proposed, with that by Potter et al. (2010) considered the most comprehensive. It states that “an estuary is a partially enclosed coastal body of water that is either permanently or periodically open to the sea and which receives at least periodic discharge from river(s), and thus, while its salinity is typically less than that of natural sea water and varies temporally and along its length, it can become hypersaline in regions when evaporative water loss is high and freshwater and tidal inputs are negligible.”

Tweedley et al. (2016) argue that tidal range, and thus the magnitude of tidal water exchange, is a “master factor” governing the flushing of these systems. Therefore, estuaries are categorised as either macrotidal (maximum tidal range > 4m), mesotidal

(maximum tidal range 2-4 m) or microtidal (maximum tidal range < 2 m). Given the large volumes of water exchanged between a macrotidal estuary and the ocean on a tidal cycle , e.g. 14 m in the Severn Estuary (UK) (Plenty et al., 2018), they retain a permanent connection to the ocean (Elliot and McLusky, 2002; Potter et al., 2010; Bolanos et al., 2013). Macrotidal estuaries are generally found in temperate regions of the Northern Hemisphere, e.g. North America and Western Europe, and also typically receive

1 freshwater discharge throughout the year (Elliot and McLusky, 2002). In contrast, the reduced tidal water movement in microtidal estuaries, when combined with periods of low precipitation (Hodgkin and Hesp 1998; Hallett et al., 2018), results in these systems becoming periodically isolated from the ocean by sandbars formed by the along-shore and on-shore movement of sand (Ranasinghe and Pattiaratchi 1998; Chuwen et al., 2009; Hoeksema et al., 2018). Thus, macrotidal and microtidal estuaries function quite differently (Tweedley et al., 2016).

Commensurate with the diversity of estuaries and the habitats they comprise, a wide range of fish species utilise these systems. In order to enable the rigorous comparison and standardisation of the biology and ecology of different fishes in estuaries throughout the world, Elliott et al. (2007) developed a guild approach describing community structure and function. This comprises three suites of guilds i.e. estuarine usage; feeding mode and reproductive mode. The first of these was further refined by Potter et al. (2015), who assigned estuarine fish into four broad categories, namely marine, estuarine, diadromous and freshwater, to account for the species that complete their entire life cycle within the estuary, those that use it as a migratory route and those species whose juveniles use it as a nursery area (Table 1.1).

Due to their high rates of biological production from receiving large quantities of organic matter from allochthonous (generated from outside the system and transported into the estuary) and autochthonous sources (generated from processes within the estuary such as microbial degradation of phytoplankton) (Wilson, 2002; Kumar and Sarma, 2018), there is an abundance of resources and complex habitats in estuaries, providing food and shelter to many fish species for all or part of their life-cycle (Taylor et al., 2005). Therefore, estuaries support many fisheries, contributing to their high economic value (Wilson, 2002; Blaber et al., 2000). For example, in Australia, over 75% of commercial and up to 90% of recreational species, spend part of their life-cycle within estuaries (Copeland and Pollard, 1996; Lloyd, 1996; Bryars et al., 2003; Jerry, 2013). Furthermore, Elliott and Hemmingway (2002) found that 37% of all European commercial fish species used estuaries at some stage of their life-cycle. It is therefore

2 unsurprising that a review on the economic value of the world’s ecosystems estimated that estuaries have the highest total value per hectare (Costanza et al., 1997). Recreational fishing is also an integral component of estuarine fisheries and is a popular activity that provides social and economic benefits globally (ABARES, 2018). In Australia, the recreational fishing industry is particularly important to the economy and was estimated to be valued at $AU1.8 billion in 2001 (Henry and Lyle, 2003), approximately the same amount as the value of commercial fisheries (ABARES, 2002). Therefore, as estuaries provide nursery areas for many fish species that are dependent on them for early development, the exploitation by recreational and commercial harvesting in these systems has warranted an overview of management options worldwide (Whitfield, 1994; Lamberth and Turpie, 2003).

Table 1.1: Description with an example from south-western Australia of each of the four categories of fish found in estuaries given in Potter et al., (2015).

Category Description Examples Sea Mullet (Mugil cephalus) Marine Species that spawn at sea.

Black Bream Species with populations in which the (Acanthopagrus butcheri) Estuarine individuals complete their life cycles within the estuary.

Pouched Lamprey (Geotria australis) Species that migrate between the sea Diadromous and freshwater.

Minnow (Galaxius truttaceus) Freshwater Species that spawn in freshwater.

1.2. Threats to estuaries

Despite the widely recognised value of the ecosystem and socio-economic services provided by estuaries around the world, these systems have suffered high rates of biodiversity loss throughout the Anthropocene (Rolls et al, 2014), with Jackson et al. (2001) regarding temperate estuaries among the most degraded of all aquatic

3 ecosystems. Estuaries have long been subjected to anthropogenic influences as they were initially attractive to humans as they provided an abundant source of food, both within their waters and through the development of agriculture in the surrounding fertile catchment (Wilson, 1988; 2002). They subsequently became harbours for ships, allowing for the import and export of goods resulting in the establishment of permanent settlements and heavy industry on their banks (Potter et al., 2015b). Such urbanisation and agriculture resulted in dredging, coastline reshaping, dam construction, and water diversion; leading to habitat loss and fragmentation (Teichert et al., 2017). This is particularly important as, due to their strong longitudinal gradients, favourable habitats can be separated by areas of unfavourable habitat, and thus maintaining connectivity is fundamental in regulating the distribution and abundance of organisms by promoting resilience to environmental disturbances (Rolls et al., 2014; Valesini et al., 2018). Moreover, modification of the catchment development through agriculture may also lead to the development of drainage networks, increasing run-off, and eutrophication from fertilisers and other inorganic materials (Lotze et al., 2006; Winberg and Heath, 2010).

Modifications to the estuary and catchment can exacerbate the severity of stochastic events associated with climate change, such as drought and flooding, fragmented habitats and eutrophication, thus increasing the threat to global biodiversity (Coleman et al, 2018). Moreover, the intensification of storm surges, combined with rising sea levels resulting from climate change, is a major threat to low- lying coastal areas (Irish et al., 2014). For example, sea level in Fremantle in south- western Australia has risen by an average of 1.4 mm per year from 1966 to 2009 and is predicted to increase by 280 to 660 mm by 2090, under RCP4.5 (Hope et al., 2015). Such rising sea levels and the resultant storm surge events have already increased 3-fold since 1950 and are predicted to increase by 100- to 1000-fold following a 500 mm rise in mean sea level (Church et al., 2006; Hallett et al., 2018).

1.3. Instream barriers Climate change is projected to cause ongoing sea level rise that will necessitate effective mitigation strategies to protect low-lying regions from increased frequency and intensity of storm surges (see Fig. A1; IPCC, 2018). A common strategy to counteract storm surges in low lying areas is the construction of instream barriers to mitigate the risk of flooding (Irish et al., 2014; Boon and Mitchell, 2015; Du et al., 2016; Kraft et al.,

2019). Large structural barriers, such as storm surge barriers are usually vertical concrete structures with steel flaps, that can open seaward on an ebb tide and shut on a flood tide (Winberg et al., 2010; Boys et al., 2012). These allow for the outflow of freshwater from the estuary, but prevent the ingress of saline water (Indraratna et al., 1999), thus mitigating flooding risk (Fig. 1.1). Some of the largest storm surge barriers in the world include those in the Ooserchelde Estuary in the Netherlands, the Inner Harbor Navigation Canal in New Orleans, the Thames Flood Barrier in London and MOSE

(Modulo Sperimentale Elettromeccanico, Experimental Electromechanical Module) in Venice; all of which were constructed in coastal cities susceptible to hurricanes and/or storm surge events (Shaw, 1983; Smaal and Nienhuis, 1992; Stone et al., 1997; Morabito et al., 2014;). These structures are also a predominant form of tidal restriction in coastal wetlands of Australia (Williams and Watford, 1997).

While the protection that instream barriers provide is undeniable, they can come at an ecological cost (Du et al., 2016). Such barriers are known to alter hydrology, restrict tidal influence, fragment habitats, reduce movement of fauna, alter food webs and modify sediment transport (e.g. Daiber 1986; Streever 1997; Kroon and Ansell, 2006; Boys et al., 2012). Due to the importance of estuaries as nurseries for some juvenile fish and invertebrate species, as well as migration routes for diadromous species, the loss of connectivity within these systems from instream barriers compromises ecological function (Meynecke, 2009). Commensurate to this, the loss of connectivity prevents faunal movement to more favourable environmental conditions (Meynecke, 2009). Furthermore, restricted water movement allows for the

5 accumulation of nutrients, often causing large algal blooms and hypoxia that can, under particular conditions, lead to fish kill events (Keipert et al., 2008; Tweedley et al., 2017).

With the increasing threat of climate change, estuarine habitats in many parts of the world are likely to become even more fragmented due to the heightened need for the construction of instream barriers (Vinagre et al., 2011). Therefore, storm surge barrier remediation may play an important role in reducing habitat fragmentation and loss (Boys et al., 2012). Such remediation should encompass structural and/or operational changes to increase flushing and connectivity between habitats (Pollard and Hannan, 1994; Boys et al., 2012). For example, floodgates can be opened to enable flushing during non-flood times to improve water quality upstream, and fish gates (i.e. purpose built structures designed to enable fish to passage through instream barriers) can be installed to facilitate fish passage past the barrier (Cooke and Hinch, 2013).

However, for these structural changes to be effective, barrier operation should take into account specific faunal life-history characteristics, hydrological processes, habitat requirements and other ecological traits (Boys et al., 2012), and therefore monitoring is required to understand the specific needs of target species in order to mitigate ecologically detrimental impacts.

Fig 1.1. An example of an estuarine barrier, designed to control the exchange of water between the freshwater environment of Lake Alexandrina [top right] and the saline (and potentially hypersaline) environment of the Coorong Lagoon [bottom left] in South Australia. Photograph: James Tweedley.

1.4. South-western Australian estuaries

Most (82%) estuaries in south-western Australia become closed off to the ocean periodically by the formation of a sand bar at their mouths (Tweedley et al., 2016), as do a similar percentage in South Africa (Harrison and Whitfield, 2006). South-western

Australia experiences a Mediterranean climate, typified by cool, wet winters and hot, dry summers (Hill and Ryan, 2002). As 70-80% of rainfall occurs between May and September (Hodgkin and Hesp, 1998; Crisp et al., 2018), freshwater discharge is highly seasonal (Hoeksema and Potter, 2006; Tweedley et al., 2018). It has recently been recognised that microtidal estuaries in Mediterranean climates, such as those in south- western Australia, are particularly susceptible to anthropogenic impacts (Warwick et al., 2018). This is due to the compounding effects of limited (or no) tidal flushing, highly seasonal climate, long residence times and photoperiod and elevated temperatures during summer, often resulting in phytoplankton blooms, hypoxia and, on occasions, mass fish kills (Tweedley et al., 2016; 2017). Furthermore, in recent decades, freshwater 7 discharges into these estuaries have declined markedly following reductions in rainfall, which has led to the declining health of many estuaries in south-western Australia (Tweedley et al., 2014; Cottingham et al., 2018). This has had a negative impact on the fauna within these systems, particularly obligate estuarine species (Tweedley et al., 2018).

1.5. Acanthopagrus butcheri The Black Bream Acanthopagrus butcheri is an obligate estuarine sparid endemic to estuaries of southern Australia (Hindell, 2007). It can attain lengths of 600mm, weigh up to 4 kg and live for 30 years, unlike the other obligate estuarine fishes found in these in systems, that are small and short-lived, e.g. Atherinidae and Gobiidae, (Scott et al., 1974; Cadwallader and Backhouse, 1983; Hoeksema et al., 2006; Potter et al., 2008). It is therefore unsurprising that A. butcheri is one of the most recreationally and commercially important finfish species in southern Australian estuaries (Sarre and Potter, 1999; Hoeksema et al., 2006). However, as A. butcheri typically completes itslife- cycle within a natal estuary, its genetic composition differs among systems (Chaplin et al., 1997), therefore, if any perturbation was to occur, populations within an estuary are unlikely to be supplemented from stocks outside (Tweedley et al., 2014). Tagging studies have investigated the broad movement patterns of A. butcheri and demonstrated that it is capable of travelling several kilometres in a day (Hindell et al.,

2008; Sakabe and Lyle, 2010; Cottingham et al., 2015), yet typically reside in the sheltered upper estuary and spawn there during spring and early summer (Sarre and

Potter, 2000; Nicholson et al., 2008; Williams et al., 2012; Cottingham et al., 2014).

However, no studies have investigated the fine-scale movement patterns of the species nor the extent to which instream barriers influence the movement patterns of this species. Given the life-history characteristics of this species and its large body size, A. butcheri is an ideal model for investigating the impact of surge barriers on the movement of estuarine fish, particularly in response to changing environmental conditions.

1.6. Aims and hypotheses While the ecological impact of surge barriers in estuaries is well recognised (e.g. Lotze et al., 2006; Boys et al., 2012; Du et al., 2017) this study will be one of the first to specifically quantify the upstream and downstream passage of an estuarine fish through a surge barrier (including timing, direction and velocity of passage), using A. butcheri as the model species.The study will also be the first to assess how the fine-scale movement of an obligate estuarine fish through a surge barrier is related to the prevailing environmental conditions and its life-cycle, using the Vasse-Wonnerup Estuary in south- western Australia as the study site. Thus, the study had the following aims:

1. Understand fine-scale movements of A. butcheri through a surge barrier.

2. Determine conditions for movement of A. butcheri through a surge barrier.

3. Develop an operational understanding of the surge barrier to mitigate fish kills in

the future.

It is hypothesised that the movement patterns of A. butcheri through the surge barrier will be influenced by hydrological and environmental factors in conjunction with life-history traits, in particular, its spawning cycle. The study aimed to have direct management implications for refining the operation of the surge barrier to enhance fish passage and thus mitigate the risk of fish kills.

2. Materials and Methods

2.1. Study site

The Vasse-Wonnerup Estuary is located near the City of Busselton on the southern portion of the Swan Coastal Plain in south-western Australia (Fig. 2.1). It is a shallow, intermittently-open, nutrient-enriched system with two main basins (Vasse and

Wonnerup estuaries) and a channel (Wonnerup Inlet), which is intermittently open to the Indian Ocean (Fig. 2.1; Brearley, 2005; WRM, 2007; Tweedley et al., 2017). The estuary was listed as a Wetland of International Importance at the 1990 Ramsar

Convention due to its importance as water bird habitat, as it contains over 37,500 birds from ~90 species including up to 16 migratory species a year (Lane et al., 2007).

In its natural state, the Vasse-Wonnerup received discharge directly and indirectly from numerous rivers including the Capel, Ludlow, Abba, Sabina, Vasse, Iron Stone Gully, Buayanyup and Carbunup (WRM, 2007). However, the structure and hydrology of the estuary has undergone extensive anthropogenic modification since European settlement (Table A1) due to the risk of flooding to the City of Busselton. This has resulted in the system now only receiving ~20% of flow prior to catchment modifications being undertaken and so it is no longer representative of its natural form (Lane et al., 1997; DWER, 2019). Furthermore, salinities in the basins can exceed 130 ppt as a result of the limited freshwater discharge entering the system in summer and autumn, and the shallow bathymetry and subsequently high evaporation, (Tweedley et al., 2014; Fig. 2.2). These extreme conditions make the Vasse-Wonnerup one of the most hypersaline estuaries in Western Australia, only exceeded by the Hamersley and

Culham inlets on the south coast of the state (Hoeksema et al., 2018, Tweedley et al., 2019).

Fig. 2.1. (a) Denotes the location of the Vasse-Wonnerup Estuary in Australia. (b) Map of the Vasse- Wonnerup, showing the location of the study site: the Vasse surge barrier. (c) Photograph showing the difference in water quality between the eutrophic upstream (bottom of picture) and healthy downstream (top of picture) waters of the Vasse surge barrier and (d) the Vasse surge barrier, photo provided by DWER.

Geographe Bay is regarded as one of Australia’s most vulnerable stretches of coastline to the future potential impacts of sea level rise, extreme storm surge events and coastal flooding (Fig. 2.3; Kay et al., 1994, Jones et al., 2005). For example, medium to high confidence predictions demonstrate that the intensity of heavy rainfall will increase thus increasing the severity of storm surge events (Hallett et al., 2018). Furthermore, autumn and winter rainfall in the south-west has declined by 15-20% since the 1970s (Hope et al., 2015), and this is projected to decline by a further 6% by

2030 under representation concentration pathway 4.5 (RCP4.5) (Hallett et al., 2018), whereby efforts to curb greenhouse gas emissions remain the same as they are currently (DEE, 2018). Due to its shallow nature (Tweedley et al., 2017), the Vasse- Wonnerup Estuary is highly susceptible to the secondary effects of increased air and sea surface temperatures combined with decreased rainfall; including a rise in salinity through evaporation (Hallett et al., 2018).

The effects of climate change on the Vasse-Wonnerup Estuary have been exacerbated by a long and continued history of urbanisation and agricultural use in the surrounding land since European settlement in 1832 (Heath and Windberg, 2010; Boys et al., 2012). Due to the favourable conditions for human settlement, i.e. access to freshwater, fertile soils and land for grazing cattle, extensive land clearing has occurred over the past 130 years (WRM, 2007), contributing to run-off of large amounts of fertiliser from agricultural land combined with animal waste from pastures (Tweedley et al., 2017). Consequently, this system was recognised as “the most grossly enriched major wetland system known in Western Australia’’ (McAlpine et al., 1989).

Fig 2.2.: Two-dimensional plots of salinity and water depth AHD (Australian Height Datum) (m) across

the Vasse-Wonnerup in each season between March 2017 and March 2018 (Tweedley et al., 2019b). Note the hypersaline conditions upstream in the Vasse and Wonnerup Estuaries during March 2018,

and the lack of halocline development just upstream of the Vasse surge barrier compared with their presence in the Wonnerup Inlet in October 2017.

2.2. Surge barrier and fish fauna The City of Busselton was built on low-lying land and therefore, in order to prevent flooding, two surge barriers, the Wonnerup Surge Barrier and the Vasse Surge Barrier (VSB), were built in 1908 at the confluence of the two rivers with the basins (Lane et al.,

1997; Tweedley et al., 2017). The VSB was refurbished in 1927, 1942 and in 1991, the latter in response to the system’s Ramsar listing. In 2004, the barriers were replaced due to the seepages of saline water into the respective estuaries. Anthropogenic

13 pressures, such as those mentioned above, have led to numerous deleterious impacts on the ecological health of the Vasse-Wonnerup Estuary. Major toxic algal blooms and extreme hypoxia often occur causing mass fish kills; with at least nine of these events occurring between 1984 and 2013 (Lane et al., 1997; Hart, 2014; Beatty et al., 2018).

While crucial for protecting low lying land from storm surges, the VSB was thought to act as a trap for fish directly upstream of the barrier during late summer and autumn when water quality usually deteriorates (Fig. 2.1c; Beatty et al., 2018). Consequently, when the latest barrier was constructed in 2004, it included a vertical- slot fish gate, which consists of a concrete channel extending from the top of the surge barrier (headwater) to the base (tailwater) (DAF, 2019; Fig. 2.1d). The fish gates (4 m in length by 0.4 m wide) were designed so that they can be left open for extended periods without the risk of seawater flooding the estuary, and can be operated remotely (WRM,

2007; Fig. 2.4). However, it is highly likely that these fish gates have not been operated at maximum ecological efficiency with the majority of recent fish kills occurring upstream of the VSB. This was particularly evident in April 2013 when a large fish kill (> 30,000 fish) occurred in that region, with A. butcheri and the mullets Mugil cephalus and Aldrichetta forsteri being the most prevalent species (Kath Lynch, DWER, pers. com.). This resulted in the instigation of an ongoing bi-annual survey of the fish communities, with particular emphasis on the population viability of A. butcheri (Fig.

2.5a) whose population cannot be naturally replenished from outside sources (Cottingham et al., 2015b; Tweedley et al., 2018). However, there remains a lack of understanding of the passage of fish movement through the VSB and this information is critical for refining its operation to facilitate fish passage and mitigate future fish kill events.

Fig. 2.3. (a) Map showing the predicted inundation of Busselton with a sea level rise of 1.1 m, a 100 year flood and worst case cyclone tack (DEE, 2018). (b) Vasse Surge Barrier protecting Busselton during a storm event where sea level was 1.6 m higher than the estuary (DWER, 2018). This highlights its major purpose of preventing major storm surges passing upstream and flooding low-lying agricultural and urban land. (c) Map showing inundated for a RCP8.5 sea level rise scenarios (0.72m) relevent to 2100 (DEE, 2018). Note: Local government boundaries shown in red. Blue shading indicates flooding for this scenario; green shading indicates LiDAR available, not flooded for this scenario; and no shading indicates no LiDAR available (DEE, 2018).

Fig. 2.4. a) Conditions at the Vasse surge barrier during the high flow period in winter-spring showing the one-way surge barriers pushed open. b) Conditions at the barrier during summer-autumn when the fish gate is operational. Photograph taken from the upstream side of the barrier. N.B. the slot boards in place either side of the fish gate allowing water to flow upstream from the Wonnerup Inlet into the Vasse Estuary. N.B. the higher water level on the downstream side of the surge barriers during summer-autumn, the blue arrows represent direction of flow (from Beatty et al., 2018).

Fig. 2.5. Photographs showing (a) Acanthopagrus butcheri (Black Bream), (b) downstream antenna on the fish gate, (c) the insertion of a PIT tag into the body cavity of an A. butcheri and (d) the antenna controller equipment. (a) and (d) taken by Alan Cottingham and Stephen Beatty, respectively.

2.3. Sampling regime The VSB was fitted with a custom designed passive integrated transponder (PIT) antenna system at both the upstream and downstream ends of its fish gates in April

2017 (Fig. 2.5b). A total of 322 A. butcheri greater than 100 mm in total length were caught in a 21.5 m seine net in three sampling trips between March 2017 and February 2018. Each fish was tagged using Biomark 12 mm half-duplex pre-loaded PIT tags, inserted into the body cavity (Fig. 5c). These tags were employed as they are quick and easy to use, have a life-span of 20 years and can be detected by the antenna at a rate of 14 detections/second at a range of up to 200 mm from the antenna, which was confirmed using a test tag.

Fish detection data were recorded over 438 days between 20th March 2017 and 31st May 2018. Each PIT tag detection was classified as either an approach to the fish gate or upstream or downstream passage through the fish gate. An approach was thus

17 defined as a PIT tag being detected at only one antenna and a passage defined as a PIT tag being detected once at each antenna sequentially (Fig. 2.6). While data on the number of approaches was collected for the entire study period, passage data was only available from 1st November 2017 (212 days) as this was the onset of the fish gate opening period.

Upstream antenna (D2)

Downstream antenna (D1)

Fig. 2.6. Diagrammatic representation of the potential detections of fish around and through the fish gate. (a) Downstream antenna approach (PIT tag only detected at D1) (b) Successful upstream passage (i.e. PIT tag detected at D1 and D2. N.B. upstream approaches, and successful downstream passages are the reverse of (a), (b), respectively.

2.3.1. Environmental variables A suite of environmental variables was measured over the study period that were likely to explain the approaches and upstream and downstream passages through the fish gate on the VSB (e.g. Sarre, 1999; Cottingham et al., 2015b; Beatty et al., 2018; see 2.4 Statistical analyses). The environmental data used over the entire study period comprised maximum daily air temperature (used as a proxy for water temperature), mean sea level pressure, solar irradiation and moon illumination recorded for Busselton (BoM, 2018); salinity, dissolved oxygen concentration, floodgate discharge and water level recorded above and below the VSB (Eduardo de Silva, pers. comm.); and the sandbar status (i.e. a binary measure of whether or not the Wonnerup Inlet was connected to the Indian Ocean) (C. Piggott, pers. comm.).

In addition to the above variables that were measured for the entire study period, several other environmental variables were obtained that were likely to influence the daily fish passage during the major fish gate operation period (i.e. 1st November 2017 to 31st May 2018). To determine the potential effect of the hydrological conditions on daily fish passage through the fish gate, water levels upstream and downstream of the surge barrier were sourced from DWER gauging stations that recorded water levels every 5 to 45 minutes. A binary measure of whether or not water levels equalised (i.e. were the same on each side of the VSB) each day of the study was then determined. In order to determine whether the patterns of fish passage were influenced by low levels of oxygen upstream of the VSB, the minimum daily dissolved oxygen levels were measured upstream of the VSB (Eduardo de Silva, pers. comm.). Mean daily sea level pressure and percentage daily moon illumination were also sourced (BoM, 2018) in order to determine their potential influence on fish passage.

To determine the factors explaining the fine temporal scale (i.e. hourly) patterns of passage downstream and upstream during the major fish gate operation period (i.e.

1st November 2017 to 31st May 2018), the hour of individual passages (i.e. between 1 and 24) were ascertained. In addition, the minimum hourly dissolved oxygen levels were recorded upstream of the barrier (Eduardo de Silva, pers. comm.).

Table 2.1. Predictor variables (environmental and hydrological) and their units measured between 20 March 2017 and 31 May 2018, and the sources of the information.

Predictor Variables Data source

Maximum air temperature (°C) BoM Daily mean sea level pressure (hPa) BoM Change in daily mean sea level pressure (hPa) BoM Salinity (ppt) DWER Dissolved oxygen (% sat) DWER Solar irradiation (W/m2) BoM Moon illumination (%) BoM Water level either side of barrier (m) DWER Floodgate discharge (L) DWER Sandbar (open/ closed) Water Corp

2.3.2 Hydrological conditions of fish passage To investigate the hydrological conditions within the fish gate at times of tagged A. butcheri passage compared to the overall mean conditions throughout the fish gate operational period (i.e. 1st November 2017 to 31st May 2018), several metrics were examined. In order to determine the water velocity experienced by the fish passing through the fish gate, the relationship between the head difference across the VSB and water velocity was modelled. This was achieved by measuring the absolute velocity within the fish gate over a range of water level differences across the VSB over a tidal cycle (that altered the water levels downstream of the VSB). A range of models were then compared relating velocity to head difference and the model with the greatest R2 value was selected as the best fit of the data. Subsequently, the mean absolute head difference across the VSB during fish passage was calculated by matching the time of passage of each individual to the nearest available upstream and downstream water level measurements. The overall mean absolute hourly water level difference across the VSB throughout the study was also determined. The absolute water level differences were then converted into velocities and box plots generated to visually compare the mean velocity within the fish gate during times of passage compared to the available water velocities throughout the major fish passage period.

The mean time taken to pass through the fish gate was determined by examining the difference in detection times for each passage and overall mean groundspeed of 20 passage calculated by dividing the length of the fish gate chute (4 m) by the time taken to passage. Overall speed through water of all passages was also determined by the adding the modelled water velocity at the time of each passage to the ground speed of each individual and a mean calculated for all passage events (Somerton and Weinberg, 2001).

2.4. Statistical analyses Five response variables were analysed to determine how environmental conditions influenced the movement and thus temporal patterns of A. butcheri detection at the

PIT antennae on the fish gate at the VSB. The response variables included the proportion of tagged A. butcheri that: 1) Approached the downstream side of the VSB fish gate daily; 2) Passaged downstream through the VSB fish gate daily;

3) Passaged upstream through the VSB fish gate daily; 4) Passaged downstream through the VSB fish gate hourly; 5) Passaged upstream through the VSB fish gate hourly.

All statistical analyses described below were conducted using the package mgcv (Wood, 2017) in R (Studio version 1.1.456, 2018; R Core Team, 2018).

2.4.1. Generalised additive mixed models

Generalised Additive Mixed Modelling (GAMM) was selected to analyse the data as it enables approximation of the relationship between the predictor and response variables without the assumption of linearity (e.g. to account for time series data), can include both categorical and continuous variables, use error distributions other than Gaussian for responses (e.g. binary or count data), and incorporate hierarchical model structures (i.e. include random effects) or autocorrelation estimates to account for spatially or temporally non-independent data (e.g. time series data). Thus, in order to include potentially non-linear relationships between predictor and response variables, five analyses were conducted using GAMMs to determine the effects of the environmental variables on the proportion of tagged A. butcheri that satisfied each of 21 the above five responses. All analyses assumed a binomial probability distribution and included the addition of the proportion of tagged fish at liberty on each day or hour as the denominator to model proportional data.

As it was highly likely that both daily and hourly PIT detection data would be temporally correlated, correlograms were produced to examine the level of first order temporal autocorrelations in the time series data. As autocorrelation with a one-day or one-hour lag was detected in all datasets, an autocorrelation term (corAR1) was added to account for the lack of temporal independence of the PIT data (Pinheiro and Bates, 2000). Therefore, day of experiment was added as the time covariate for the daily approach or passage models, and hour of experiment added for the hourly passage GAMMs.

Initially, global GAMMs were produced for each of the five analyses using the package mgcv in the R software package. To avoid over-fitting the data in model construction (Burnham and Anderson, 2010), pairwise correlations of predictor variables that revealed maximum air temperature was positively correlated with both solar irradiation and water temperature below the VSB. Therefore, the latter two variables were removed from the subsequent analysis to avoid inclusion of correlated predictor variables. The global GAMMs that were then produced included all predictor variables listed for the approaches model (Table 2.2), each of the downstream and upstream daily passages (Table 2.3), and each of the hourly downstream and upstream daily passages (Table 2.4).

For the daily approach and passage models, global models were initially fitted and were used to produce a set of all possible models using the package MuMIN in R (Bartón, 2013), which were then ranked according to Akaike’s Information Criterion

(AICC). A subset of top ranked models (i.e. those within 4 AICc from the best fit model) were produced and then each predictor variable’s importance was determined by summing the AIC weights across all best fitting models involving that variable. The value produced was thus the probability of each variable being present in the AIC best model. In order to visualise the effects of the smoothed terms, the best fit (reduced) model 22 from each of the five analyses was again tested for temporal autocorrelations and a GAMM produced, and the smooth terms plotted. As there were a limited number of predictor variables that were included in the GAMM of the hourly passage, and all were directly associated with key hypotheses of the study relating to the response of A. butcheri movement patterns to depleted water quality and hydrology, all were included in the final model.

Table 2.2: Description of the predictor variables used in the GAMM analyses of daily proportion of tagged A. butcheri that approached the Vasse Surge Barrier fish gate.

Variable name Variable type Variable code

Connection of Vasse-Wonnerup to the ocean Nominal binary (open or closed) Sand Bar Daily percentage moon illumination Continuous (smoothed) sMoon Daily discharge through the surge barrier Continuous (smoothed) sDischarge Mean daily air pressure Continuous (smoothed) sPressure Change in daily air pressure (change from sChange in Continuous (smoothed) previous day) pressure Maximum air temp Continuous (smoothed) sTemp Daily mean salinity downstream of surge Continuous sSal barrier Daily minimum dissolved oxygen Continuous sDOmin downstream of surge barrier Daily mean dissolved oxygen downstream of Continuous sDOmean surge barrier

Table 2.3: Description of the predictor variables used in the GAMM analyses of daily proportion of tagged A. butcheri that passaged downstream or upstream through the fish gate on the Vasse Surge Barrier.

Variable name Variable type Variable code Equalisation of water level upstream and Nominal binary (equalised or did Equalised downstream of barrier not equalised) Daily minimum dissolved oxygen upstream Continuous DO of surge barrier Daily percentage moon illumination Continuous (smoothed) sMoon Mean daily air pressure Continuous (smoothed) sPressure Change in daily air pressure (change from sChange in Continuous (smoothed) previous day) pressure Maximum daily air temp Continuous (smoothed) sTemp

Table 2.4: Description of the predictor variables used in the GAMM analyses of hourly proportion of tagged A. butcheri that passaged downstream or upstream through the fish gate on the Vasse Surge Barrier.

Variable name Variable type Variable code

Hour of passage (i.e. between 1 and 24) Continuous (smoothed) sHour Hourly minimum dissolved oxygen upstream Continuous DOhr of surge barrier Absolute mean hourly water level difference upstream and downstream of the Vasse Continuous WL surge barrier

3. Results

3.1. Environmental variables

Maximum air temperature was higher between late spring to early autumn (November to March), reaching a maximum of 39.8°C during summer, and was lower during winter (June to August), with a lowest value of 12.7°C recorded in July 2018 (Fig. 3.1). Mean sea level pressure ranged from 994.44 to 1032.73 hectopascals (hPa) and was highly variable among months, particularly between March to November 2017 (Fig. 3.1). Solar irradiation ranged from 2.2 to 31.7 W/m2 and was generally greatest in the warmer months (November to March) and lowest in the cooler months (May to September) (Fig. 3.2). Moon illumination maintained a constant trend across lunar months, peaking approximately every 28 days before decreasing to the cycle’s minimum approximately 14 days after that (Fig. 3.2).

Mean salinities above the VSB remained relatively constant at 35 - 40 parts ppt from March to July 2017 after which they declined to a minimum of ~ 0 ppt during August, before fluctuating between September and December 2017, when salinities returned to 35 - 40 ppt for the remainder of the study (Fig. 3.3). Mean daily dissolved oxygen concentration measured as percentage saturation (% sat) above the fish gate ranged between 35 and 185, and daily minimums were lowest during August 2017 and at intervals during the summer months (Fig. 3.4). The fish gate was opened on 1st November 2017 and following this event, median dissolved oxygen concentrations peaked during the afternoon (~100%) and were lowest at night and around sunrise (~60%; Fig. 3.5).

From November 2017 to May 2018 water level on the downstream-side of the VSB ranged between ~-0.2 and 1.3 m above sea level, while the upstream-side ranged between ~0 and 0.4 m. The greatest difference between the two water levels occurred in late-May 2018, when it exceeded 1 m on two consecutive days (24th and 25th). Water levels equalised for varying periods each month, with mid-May 2018 having the most consecutive days whereby water level equalised on both side of the VSB (Fig. 3.6).

Mean sea level pressure (hPa) pressure level Mean sea Maximum air temperature ( temperature air Maximum

Fig. 3.1: Daily maximum air temperature (°C) [blue] and daily mean sea level pressure (hPa) [orange] recorded between 20th March 2017 and 31st May 2018 at Busselton. Data sourced from BoM (2018).

)

Moon illumination (%) illumination Moon Sun irradiation (W/m irradiation Sun

Fig. 3.2: Solar irradiation (W/m2) [blue] and moon illumination (%) [orange] recorded between 20th March 2017 and 31st May 2018 at Busselton. Data provided by BoM (2018).

Daily mean salinity concentration (ppt) concentration salinity mean Daily

Fig. 3.3: Mean daily salinity (ppt) recorded between 20th March 2017 and 31st May 2018 downstream of the Vasse Surge Barrier. Data provided by DWER.

Dissolved oxygen content (% saturation) (% content oxygen Dissolved

Fig. 3.4: Mean [blue] and minimum [orange] daily dissolved oxygen content (percentage saturation) recorded between 20th March 2017 and 31st May 2018 downstream of the Vasse Surge Barrier. Data provided by DWER. The red line indicates when the Vasse Surge Barrier fish gate was opened (1st November 2017).

Dissolved oxygen content (% saturation) (% content oxygen Dissolved

Fig. 3.5: Hourly dissolved oxygen content (percentage saturation) recorded between 1st November 2017 and 31st May 2018 upstream of the Vasse Surge Barrier. Data provided by DWER.

Fig. 3.6: Mean hourly water level difference (m) across the Vasse Surge Barrier (i.e. downstream water level minus upstream water level) recorded between 1st November 2017 and 31st May 2018. Data provided by DWER.

3.2. Factors influencing approaches to the Vasse Surge Barrier The highest proportion of daily approaches (i.e. detection at the antennae on the downstream end of the fish gate without subsequently passaging through the gate) of tagged A. butcheri occurred in spring 2017 and autumn 2018 (i.e. September to December and April to May, respectively (Fig. 3.7)). The daily proportion of tagged A. butcheri approaching the VSB was best explained by the GAMM containing the smoothed effects of mean salinity and minimum daily dissolved oxygen downstream of the barrier, mean daily air pressure, maximum air temperature and moon illumination (Tables 3.1 – 3.3). Probability of daily approaches were lowest at extreme low and high temperatures and salinities and were highest on days with extreme low and high air pressure (Figs. 3.8). For example, proportion of approaches over 0.08 occurred at salinities ranging from 29 to 36 ppt, and maximum daily temperatures from 21-27°C with the greatest proportion (0.09) approaching at ~30 ppt and ~25°C, respectively.

Probability of approaches generally decreased with increasing minimum dissolved oxygen levels and moon illumination (Figs. 3.8). The model explained ~26 % of the deviance.

A.butcheri Proportion of tagged tagged of Proportion

Fig. 3.7: Proportion of tagged A. butcheri that approached the Vasse Surge Barrier fish gate (downstream) recorded between 20 March 2017 and 31 May 2018. Note: Typical A. butcheri spawning period in the Vasse-Wonnerup Estuary is between July and October [red rectangle].

Table 3.1: Importance (i.e. probability of selection in best fitting model) of predictor variables for the global model explaining the proportion of tagged A. butcheri that approached the Vasse Surge Barrier fish gate (i.e. were detected at the downstream PIT antenna but did not successfully passage upstream through the fish gate). N.B. See Table 2.2 for variable codes and text for more details.

Variable Importance sSal 1.0 sPressure 1.0 sDOmin 1.0 sTemp 1.0 sMoon 1.0 sDOmean 0.09 sChange in Pressure <0.01 sDischarge <0.01 Sand Bar <0.01

Table 3.2: Results of model selection based on Akaike's Information Criterion (AIC) (i.e. models within 4 AIC of the best fitting model) explaining the daily proportion of A. butcheri that approached the Vasse Surge Barrier fish gate. N.B. there was only one model selected.

Variables df logLik AICc delta weight sDOmin + sPressure + sMoon + sTemp + sSal 12 -860.35 1745.44 0 0.911

Table 3.3: Outputs of the best fitting model to explain the proportion of A. butcheri that approached the Vasse Surge Barrier fish gate (i.e. were detected at the downstream PIT antenna but did not successfully passage upstream through the fish gate). N.B. See Table 2.2 for variable codes and text for more details. Bold p values indicate significant at p <0.01.

Estimate Std. Error t value Pr(>|t|) (Intercept) -4.40 0.04 -99.96 <0.001

edf Ref.df F p-value sMoon 1.00 1.00 20.22 <0.001 sSal 5.26 5.26 17.23 <0.001 sDOmin 5.68 5.68 8.45 <0.001 sPressure 6.95 6.95 13.84 <0.001 sTemp 3.25 3.25 6.43 <0.001

a) b)

c) d)

Fig. 3.8: The smoothed effects of: a) maximum daily air temperature, b) mean daily air pressure, c) minimum daily dissolved oxygen below the Vasse Surge Barrier, d) mean salinity below the Vasse Surge Barrier, e) moon illumination, on the daily proportion of tagged A. butcheri detected approaching the Vasse Surge Barrier fish gate.

3.3. Hydrological conditions of fish passage Over the duration of the study, water velocity within the fish gate during passage events was 0.41 (±0.0006 S.E.) m/s compared with a mean of 1.09 m/s throughout the major passage period (i.e., when the fish gate was operational) (Fig. 3.9). The overall mean groundspeed of passaging A. butcheri was 0.27 (±0.007) m/s and the mean speed through the water was 0.40 (±0.001) m/s (maximum recorded speed was 4.34 m/s).

Fig. 3.9: Box plot of absolute water velocity (m/s) within the Vasse Surge Barrier fish gate during fish passage events (left) compared to overall mean hourly water velocity (m/s) (right) over the period that the fish gate was operational.

3.4. Factors influencing daily downstream and upstream passage through the Vasse

Surge Barrier fish gate From 1st November 2017 until 31st May 2018, tagged A. butcheri passed through the VSB fish gate (upstream and downstream) 440 times. The daily proportion of tagged A. butcheri that passaged was 0.00 - 0.03 each day until early May when there were passages each day for 14 consecutive days, reaching a daily proportion maximum of 0.09 (Fig. 3.10).

A total of 265 downstream passages were completed. The daily proportion of tagged A. butcheri that passaged downstream through the VSB fish gate was best explained by the GAMM containing the smoothed effects of mean daily air pressure and

32 moon illumination and the binary factor of whether or not daily water level equalised (Tables 3.4 – 3.6; Fig. 3.10). There was a strong positive effect of daily water level equalisation such that the probability of downstream passage increased when water levels equalised across the VSB (Tables 3.4 – 3.6). Probability of daily downstream passages increased with air pressure and was variable with moon illumination, peaking on days with lower or moderate illumination levels (Fig. 3.11). The model explained

~54% of the deviance.

that passaged that

A.butcheri A.butcheri

Daily number of times water level equalised level water times of Daily number Proportion of tagged tagged of Proportion

Fig. 3.10: Proportion of tagged A. butcheri that passaged through the Vasse Surge Barrier fish gate [blue] and daily number of times water levels equalised on the upstream and downstream sides of the barrier [orange], recorded between 1st November 2017 and 31st May 2018.

Table 3.4: Importance (i.e. probability of selection in best fitting model) of predictor variables for the global model explaining the daily proportion of tagged A. butcheri that passaged downstream through the Vasse Surge Barrier fish gate. N.B. See Table 2.3 for variable codes and text for more details.

Variable Importance sPressure 1.00 sMoon 1.00 Equalised 1.00 DO 0.16 sTemp 0.14

Table 3.5: Results of model selection based on Akaike's Information Criterion (AIC) (i.e. models within 4 AIC of the best fitting model) explaining the daily proportion of tagged A. butcheri that passaged downstream through the Vasse Surge Barrier fish gate.

Variables df logLik AICc delta weight sPressure + sMoon + Equalised 7 -436.95 888.45 0 0.67 sPressure + sMoon + Equalised + DO 8 -437.38 891.46 3.01 0.15 sPressure + sMoon + Equalised + sTemp 9 -436.40 891.68 3.24 0.13

Table 3.6: Outputs of the best fitting GAMM to explain the daily proportion of tagged A. butcheri that passaged downstream through the Vasse Surge Barrier fish gate. N.B. See Table 2.3 for variable codes and text for more details. Bold p values indicate significant at p <0.01.

Estimate Std. Error t value Pr(>|t|) (Intercept) -6.31 0.17 -37.18 <0.001 Equalised 0.57 0.18 3.12 0.002

Edf Ref.df F p-value sMoon 6.05 6.05 6.58 <0.001 sPressure 1.00 1.00 92.07 <0.001

a) b)

Fig. 3.11: The smoothed effects of: a) mean sea level pressure and b) moon illumination, on the daily proportion of tagged A. butcheri that passaged downstream through the Vasse Surge Barrier fish gate.

A total of 175 upstream passages were completed. The daily proportion of tagged

A. butcheri that passaged upstream through the VSB fish gate was best explained by the GAMM containing the smoothed effects of daily change in sea level pressure, maximum air temperature and moon illumination and the binary factor of whether or not daily water level equalised (Tables 3.7 – 3.9). Probability of daily upstream passages decreased with larger changes in sea level pressure from one day to the next and with increasing maximum air temperature (Figs 3.12a; 3.12b). The effect of moon illumination was small, with a slight decrease in probability of upstream passage with increased illumination (Fig. 3.12c). There was a strong positive effect of daily water level equalisation such that the probability of upstream passage increased when water levels equalised across the VSB. This model explained ~21% of the deviance.

Table 3.7: Importance (i.e. probability of selection in best fitting model) of predictor variables for the global model explaining the daily proportion of tagged A. butcheri that passaged upstream through the Vasse Surge Barrier fish gate. N.B. See Table 2.3 for variable codes and text for more details.

Variable Importance sPressure 1.00 sTemp 1.00 Equalised 1.00 sMoon 0.85 DO 0.10

Table 3.8: Results of model selection based on Akaike's Information Criterion (AIC) (i.e. models within 4 AIC of the best fitting model) explaining the daily proportion of tagged A. butcheri that passaged upstream through the Vasse Surge Barrier fish gate.

Variables df logLik AICc delta weight Change in Pressure + Temp + Equalised + Moon 7 -436.95 888.45 0 0.67 Change in Pressure + Equalised + Temp 8 -437.38 891.46 3.01 0.15 Change in Pressure + Moon + Equalised + Temp + DO 9 -436.40 891.68 3.24 0.13

Table 3.9: Outputs of the best fitting GAMM to explain the daily proportion of tagged A. butcheri that passaged upstream through the Vasse Surge Barrier fish gate. N.B. See Table 2.3 for variable codes and text for more details. Bold p values indicate significant at p <0.01.

Estimate Std. Error t value Pr(>|t|) (Intercept) -7.19 0.26 -27.33 <0.001 Equalised 1.83 0.27 6.78 <0.001

Edf Ref.df F p-value sMoon 1.00 1.00 1.99 0.160 sChange in Pressue 1.00 1.00 21.28 <0.001 sTemp 2.63 2.63 4.14 <0.001

a) b)

Fig. 3.12: The smoothed effects of: a) daily change in sea level pressure, b) maximum air temperature and c) moon illumination, on the daily proportion of tagged A. butcheri that passaged upstream through the Vasse Surge Barrier fish gate.

3.5. Factors influencing the hourly downstream and upstream passage through the Vasse Surge Barrier fish gate The hourly proportion of tagged A. butcheri that passaged downstream through the VSB fish gate was explained by the GAMM containing the smoothed effect of hour, effect of minimum dissolved oxygen content and the binary factor of whether or not daily water level equalised (Table 3.10). Probability of hourly downstream passages decreased during the day (between 6:00am and 4:00pm) and increased in the evening to early morning hours (Fig 3.13). There was a very strong negative effect of absolute water level difference across the VSB, such that the probability of downstream passage decreased during hours when there was greater difference in water levels across the VSB. There was a slight negative effect of minimum dissolved oxygen, such that the greater the minimum hourly dissolved oxygen that was recorded above the VSB, the less likely fish were to passage downstream. This model explained 23% of the deviance.

Table 3.10: Outputs of the best fitting GAMM to explain the hourly proportion of tagged A. butcheri that passaged downstream through the Vasse Surge Barrier fish gate. N.B. See Table 2.4 for variable codes and text for more details. Bold p values indicate significant at p <0.01.

Estimate Std. Error t value Pr(>|t|) (Intercept) -5.450 0.319 -17.085 <0.001 minDO -0.024 0.004 -5.817 <0.001 WL -26.202 1.939 -13.516 <0.001

edf Ref.df F p-value sHour 6.492 6.492 15.86 <0.001

Fig. 3.13: The smoothed effect of hour of the day on hourly proportion of tagged A. butcheri that passaged downstream through the Vasse Surge Barrier fish gate.

The hourly proportion of tagged A. butcheri that passaged upstream through the VSB fish gate was explained by the GAMM containing the smoothed effect of hour, effect of minimum dissolved oxygen content and the binary factor of whether or not daily water level equalised (Table 3.11). Probability of hourly upstream passages was crepuscular; increasing around the dawn and dusk hours (Fig. 3.14). There was a very strong negative effect of absolute water level difference across the VSB, such that the probability of upstream passage decreased during hours when there was greater difference in water levels across the VSB. There was a slight negative effect of minimum dissolved oxygen, such that the greater the minimum hourly dissolved oxygen that was recorded above the VSB, the less likely fish were to passage upstream. This model explained ~7% of the deviance.

Table 3.11: Outputs of the best fitting GAMM to explain the hourly proportion of tagged A. butcheri that passaged upstream through the Vasse Surge Barrier fish gate. N.B. See Table 2.4 for variable codes and text for more details. Bold p values indicate significant at p <0.01

Estimate Std. Error t value Pr(>|t|) (Intercept) -6.380 0.324 -19.664 <0.001 minDO -0.018 0.004 -4.399 <0.001 WL -13.293 1.416 -9.388 <0.001

edf Ref.df F p-value sHour 7.298 7.298 8.703 <0.001

Fig. 3.14: The smoothed effect of hour of the day on hourly proportion of tagged A. butcheri that passaged upstream through the Vasse Surge Barrier fish gate.

4. Discussion Instream barriers such as storm surge barriers are becoming increasingly important (Du et al., 2016) for the protection of low-lying coastal infrastructure and human populations from increased flooding risk as a result of climate change (IPCC, 2018) , While the ecological impact of estuarine surge barriers on diadromous fishes, particularly salmonids, is well recognised (e.g. Swanson et al., 2013; Pess et al., 2014), this study is one of the first to quantify and analyse drivers of the upstream and downstream passage of an obligate estuarine fish through a surge barrier fish gate. Previous studies have documented broad-scale patterns of movement of A. butcheri within estuaries using acoustic telemetry (e.g. Hindell, 2007; Hindell et al., 2008; Williams et al., 2017; Beatty et al., 2018) and others have used conventional traps to determine the broad-scale movement of other fish species through fish gates (e.g. Bice et al., 2017). However, by using a contemporary passive integrated transponder system, this study has revealed how environmental and hydrological factors can influence fish passage at the individual level thereby providing invaluable information to facilitate improved operation of storm surge barriers in general to mitigate their impacts on obligate estuarine fishes.

4.1. Factors influencing the approaches of Acanthopagrus butcheri to the Vasse Surge Barrier

The movement patterns around the VSB fish gate (i.e. approaches and passages) of A. butcheri were related to several environmental factors and these relationships can be explained through an understanding of the life-history and environmental preferences of the species. Approaches at the downstream side of the VSB peaked between September-December 2017 and April-May 2018. The spawning period of A. butcheri In the Vasse-Wonnerup Estuary occurs between July and October (Cottingham et al., 2015b). As an increase in approaches to the VSB occurred late in that spawning period

(prior to the fish gate opening in November 2017), one could assume a proportion of those fish may have been associated with an upstream spawning movement. However, the species is known to favour estuarine haloclines for successful recruitment (e.g. 40

Williams et al., 2012) and does not successfully spawn upstream of the VSB likely due to the nullification of tidal flow due to the VSB; with the key spawning site being the Deadwater region (Fig. 2.1) (Cottingham et al. 2015b). Acanthopagrus butcheri are euryhaline (i.e. can tolerate a wide range of salinities, from ~0 to 60 ppt) (Hoeksema et al, 2006), and thus salinities immediately upstream of the VSB were well within their physiological tolerance for the entire study period. However, by late summer the hypersalinity that occurs in the upper Vasse Estuary (as a result of a lack of freshwater inflow, high evaporation and shallow depth), would not support A. butcheri (Fig 2.2; Tweedley et al., 2014b). Thus, the only suitable habitat upstream of the VSB during late summer and autumn, in terms of salinity, is the narrow ~3 km long channel directly upstream of the VSB. However, it is in these reaches where phytoplankton blooms and hypoxia lead to fish kills during those warmer months and at a time when the floodgates are typically closed to prevent saltwater encroaching upstream (Cottingham et al.,

2015b). Therefore, there is little benefit to A. butcheri in accessing habitat upstream of the VSB, and thus it is crucial that they can freely pass downstream during summer and autumn to escape poor water quality conditions.

Cottingham et al., (2018) deduced that availability of dissolved oxygen and nutritious food are likely the main drivers of growth of A. butcheri in south-western Australian estuaries, rather than water temperature or salinity. The preferred food items of A. butcheri are crustaceans and molluscs (Chuwen et al., 2007; Sarre, 1999), yet the Wonnerup Inlet is almost devoid of complex habitat that support the colonisation of these food items (Beatty et al., 2018). While outside the scope of the current study, it is likely that solid structures such as the VSB, may support a valuable food resource for A. butcheri in the system (Fig. A2) that is otherwise dominated by macroalgae and detritus (Cottingham et al., 2015b). Beatty et al. (2018) also suggested that the two bridges and the two surge barriers in the system would provide both shelter and support food resources for A. butcheri. There were a substantially higher proportion of approaches to the VSB in May 2018 (0.71) compared to May 2017 (0.41), that coincided with warmer daily air temperatures in May 2018 in comparison to May 2017 (BoM,

2019), implying warmer water temperature. As temperature increases, biochemical reactions proceed faster (Angilletta et al. 2002), and so the capacity for feeding and growth increases with temperature (Remen et al., 2015). Therefore, as May 2018 was warmer that May 2017, A. butcheri may have increased their foraging and feeding activity at the VSB in order to sustain their metabolic rate, hence explain the greater proportion of approaches in the former month.

During the current study, the presence of at least one Indo-Pacific Bottlenose Dolphin (Tursiops aduncus) was noted within the Wonnerup Inlet and Deadwater, downstream of the VSB (Cottingham et al., 2018b). Although the diet of this large mammal species within the Vasse-Wonnerup is not known, it is an opportunistic feeder has been observed herding mullet and A. butcheri in the system (S. Beatty pers. com.), and likely preys upon high calorific fish such as A. butcheri (McCabe et al., 2010;

McCluskey et al., 2016). Therefore, it is also possible that A. butcheri may have travelled upstream, approaching the VSB, in order to seek refuge and shelter from predation. The bridges and surge barrier habitats were also favoured by A. butcheri in the acoustic telemetry study by (Beatty et al., 2018) who also concluded that it was, in part, attributed to the provision of shelter for the species.

4.2. Factors influencing the passage of Acanthopagrus butcheri through the Vasse

Surge Barrier Diel periods can have a strong influence on fish activity and behavioural patterns, depending on various life-history traits (e.g. Hindell et al., 2008; Haraldstad et al., 2016;

Imre et al., 2017). Hourly detections of A. butcheri passaging upstream and downstream through the VSB fish gate were predominantly nocturnal and crepuscular, respectively, with the lowest detection rates recorded during the daylight hours (~6:00am to 3:00pm). These movement patterns were consistent with the Hoeksema and Potter study (2006) that likewise found A. butcheri to be most active at night. Such diel behaviour patterns have been observed in other obligate estuarine fish species e.g. Macquaria colonorum (Taylor et al., 2006) and Argyrosomus japonicus (Walsh et al.,

2013). The current study also found that dissolved oxygen content was lower at night and highest in the late afternoon, indicative of respiration and photosynthesis, respectively (Tyler and Targett, 2007). Commensurate to this, the probability of passages through the VSB increased with lower minimum dissolved oxygen levels occurring during the night. Therefore, given that A. butcheri rely on dissolved oxygen for survival (Cottingham et al., 2018b), and the waters downstream of the VSB typically have higher oxygen content (Cottingham et al., 2015b), diel fluctuations in this parameter could explain the timing of downstream passages at night. Moreover, enabling the downstream escape of severe hypoxia that can occur upstream of the VSB is critical to mitigating the risk of fish kills that have mostly occurred in that upstream habitat recently.

Hydrological conditions within the fish gate clearly influenced the probability of passage by A. butcheri. The mean water velocity at times of successful passage (between 1st November 2017 and 31st May 2018) was 0.41 m/s, which is lower compared to the overall mean water velocity (i.e. 1.09 m/s). Furthermore, the probability of passage (in both directions) increased when water levels equalised across the VSB. For example, the water levels equalised 165 times over 12 days in May 2018; more than any other month during the study period, which coincided with the highest proportion of passages (0.67; Fig. 3.10). While they did not look at fine-scale movements, Beatty et al., (2018) conducted an acoustic telemetry study and similarly found that few fish travelled through the fish gate at high flow (such as that in Fig. 2.3b) and suggested that A. butcheri in the Vasse-Wonnerup Estuary may have limited propensity to passage against the flow through fish gates. However, the latter study also concluded that successful upstream passages were likely associated with negative head differential from down- to upstream. Similarly, A. butcheri in southern and eastern parts of Australia have displayed an inhibition to pass through restricted spaces such as fish gates (McNeil et al., 2010;

Baumgartner et al., 2014, Bice et al., 2017). This has been hypothesised to be due to the narrowness of those passage structures, and the subsequent increased water velocity within them (Mallen-Cooper, 2004; McNeil et al., 2010) that may exceed the swimming

43 performance of A. butcheri, however, no literature was previously available on the species’ swimming metrics. The current findings suggest that the species indeed avoids passage through high-flow conditions, but this avoidance occurs both with and against high flows.

As morphology greatly affects the swimming performance of fishes (Webb,

1984), the above findings are likely related to the deep round body shape of A. butcheri, which unlike streamlined salmonids, are not built for great speed and navigating strong currents (Scott and Crossman, 1973). Unlike acoustic tracking, this PIT study was able to measure the speed at which A. butcheri typically swim through the fish gate. The maximum recorded being 4.34 m/s, which is the first recorded upper estimate of its swimming performance. Several studies have shown A. butcheri to be move downstream into estuary basins during winter when freshwater discharge and thus flow rates increase in the upper regions of estuaries (Sarre and Potter, 2000; Cottingham et al., 2015). Rather than a physiological inability to negotiate high-flow conditions, the response of A. butcheri to changes in flow likely relate to behavioural factors associated with its life-history. Therefore, while determining swimming performance of target species is important in the design of fish passage structures, a similar understanding of behavioural and life-history traits (such as migration and spawning periods) is also required.

4.3. Study limitations and future research

As the floodgates at the VSB were closed during the major passage period of the study, all proportions of passages recorded are indicative of those made specifically through the fish gate, therefore, the use of a PIT antenna system on either side of the VSB fish gate was highly effective in determining the fine-scale movement patterns of A. butcheri through it. However, as the antennae only detect tags within a 200 mm radius, congregations along the length of the barrier were not detected, and thus conclusions on those factors influencing the approaches to the fish gate, such as those relating to foraging behaviour, are not definitive in this study. Although there were few passages

44 through the fish gate until January 2018, the large numbers of downstream passages detected in May 2018 suggests that many fish had used the floodgates (which were open from early August 2017 until 1st November), to migrate upstream prior to the fish gate’s operation, and therefore were not detected by the downstream antenna that only monitored the narrow fish gate. Therefore, while it would be technically challenging and expensive, it would be of high value to have the entire VSB PIT monitored in order to ensure all A. butcheri that passed through the structure could be detected to increase the understanding of year-round movements. A similar PIT study at the Wonnerup Surge Barrier would also add further insight into the comparisons in fish movement at two adjoining estuaries and how they interact with the barriers.

Although there was a decrease in detection of approaches made by A. butcheri to the VSB with increases in moon illumination the magnitude of the effects was minimal in comparison to other environmental factors. Illumination provided by the moon increases light, hence allowing fish to move and forage more during the night, and thus less during the daytime (Milardi et al., 2018). As the Vasse-Wonnerup is a shallow estuary, the effects of moon illumination would likely be more evident due to the light penetrability (Tweedley et al., 2017; Milardi et al., 2018). However, as stated above, the limited detection range means that many individuals may indeed have approached the VSB, but went undetected. Therefore, the negative relationship between moon illumination and approaches found in this study may be biased and its influence on A. butcheri movement and foraging requires further investigation.

While A. butcheri approached the downstream side of the VSB more during periods of extreme high and low mean sea level pressure in comparison to intermediate pressures, there is limited literature surrounding the extent to which fish have an absolute sense of pressure, however, it is thought that swim bladders may play a role (Heupel et al., 2003). Sea level pressure affects tidal fluctuations, of which fish are entrained (Gibson, 1984), and thus Gibson (1970) suggests that fish can anticipate changes in their environment based on the variation in tidal cycles caused by the changes in pressure. However, as the Vasse-Wonnerup Estuary mouth and entrance

45 channel is narrow, and the system is microtidal (Tweedley et al., 2017), there is minimal tidal influence. Therefore, further research on the sensitivity of teleosts, specifically microtidal estuarine sparids, to mean sea level pressure and its possible influence on their movement would be beneficial as surge barrier operation could be automated in anticipation of high and/or low pressure systems, depending on the cues taken by the target species.

A key finding of this study was that A. butcheri are more likely to passage through a fish gate during times of low water velocity. As it did not tend to passage during times of both strong flow with or against its passage direction, this finding was likely due to a behavioural trait although its swimming performance has not previously been quantified. Therefore, the swimming performance of this species under differing environmental conditions (e.g. under varying levels of dissolved oxygen) are required to determine its passage capabilities. Also, PIT tagging other fish species with differing morphology, such as the mullets Mugil cephalus and Aldrichetta forsteri would add insight to the level at which body shape may play a role in a species’ inhibition to navigate through a narrow fish gate during higher water velocity within the same system. As many other estuarine systems in which A. butcheri exists are also highly regulated, and climate change continues to alter their hydrology, this research will help to determine how the design and operation of surge barriers (and indeed fish ladders on weirs) may need to consider changes in environmental conditions to enable fish passage in the future.

4.4. Management implications and recommendations This study highlights the need to consider the movement patterns of resident fishes within estuaries in order to mitigate the effects of instream barriers. For example, seasonal connectivity to favourable spawning environments is essential for many estuarine species to complete their life-cycles (Rolls et al., 2014; Valesini et al., 2018). Dissolved oxygen, salinity and temperature are also key environmental factors influencing the survival of estuarine fishes (Harrison and Whitfield, 2006; Cottingham et

46 al, 2018) thus their ability to move away from regions of poor water quality needs to be maintained or reinstated. Therefore, fish passage structures are essential on surge barriers to facilitate movement and the current study highlights that careful consideration of the passage requirements of target species is required.

Enhancing the survivability of A. butcheri, in highly regulated systems such as the Vasse-Wonnerup Estuary is of particular importance as this species has the greatest recreational value of any other finfish in south-western Australian estuaries, and plays an important role in the ecosystem (Sarre and Potter, 1999; Hoeksema et al., 2006). As A. butcheri was found to be significantly more likely to passage through the VSB during times of low water velocity within the fish gate, it is recommended that the VSB be automated and programmed to open when the water level equalises, or is slightly higher on the upstream side. This will facilitate low flow fish passage periods, while preventing the penetration of saline water upstream, thus reducing chances of stratification and subsequent hypoxia. While the current study has focused on a structure around which major kills have mostly occurred in recent times, it is also recommended that the input of nutrients from surrounding agricultural and urban landuses be addressed as they are an underlying source of the poor water that occurs in the system (WRM, 2007; DWER, 2019).

4.5. Conclusion The findings here have advanced the understanding of the environmental and hydrological drivers of A. butcheri movement patterns through an estuarine surge barrier. It was hypothesised that the movement patterns of the species would be influenced by a range of hydrological and environmental factors that could be explained by an understanding of the life-history and environmental preferences of the species. The species appeared to be avoiding periods of low oxygen upstream of the VSB with water velocity within the VSB fish gate having a pronounced influence on individual fish passage, with the species favouring conditions of low velocity within the fish gate in order to passage. Due to the dynamic nature of estuarine systems, many other

47 environmental and biological factors also play a pivotal role in the overall behavioural patterns of fishes. Understanding how fish movements are influenced by these factors is crucial in designing structures that enable fish passage through estuarine barriers. As the climate continues to change, threatening human settlement on coastal and low-lying land due to increased flooding and storm surges, instream barriers are becoming more prevalent. This study highlights the direct benefit in understanding the fine-scale movement patterns of estuarine fishes in order to mitigate the negative impact of surge barriers.

5. References

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6. Appendices

Reduced leakageReduced of salt water.

Increased leakage of salt water.

and for short periods (hours of time 1-2 to days).

Wonnerup floodgates manually on an opened as basis, needed

Guidelines strictly not adhered to.

vegetation and trees and a possible decline in birds.

Saline hypersaline to waters causing death of riparian

suitable level of freshwater for breeding swans in "Swan Lake".

Flap-valved culvert in manually levee the operatated maintain to

drying early in season. the

raise it in estuaries the in spring pastoral prevent to lands from

Reduced water levelsReduced much, too and measures taken to were

lying coastal properties.

Increased river inflow, resulting in flooding frequent more of low

Annual drying ofestuaries. most of both the

Hydrological result modification of Hydrological

Wonnerup Estuarine with Wonnerup system negative subsequent or positive

of of the Vasse

actions

results of each initiative delineated in red or green, respectively (WRM, (WRM, 2007). respectively green, or red in delineated initiative each of results

fish gates which can controlled remotely be by telemetry.

Surge Surge barrier upgraded by replacing entire structure the with concrete and installed small

winter 1997.

provide 1:100 year flood protection in response flooding to of Busselton Township during

Detention basinsDetention in upper Vasse River catchment and minor upgrade of Diversion Drain to

gates.

Water Corporation upgraded floodgates by replacing gates wooden with the stainless steel

Stricter adherence 1990 to guidelines.

water entry.

Operational guidelines floodgates for the revised Water by the Corporation limit to salt

Manual opening of Vasse floodgates summer-autumn openings. extend to implemented

Naturalist Club ameliorate to poor water quality and mass fish kills.

Campaign for manual openings of floodgates over-summer autumn to lead by Busselton

which had diverted south been levee. of the

Levee bank constructedLevee at Wonnerup Estuary back-flooding prevent to by Ludlow River

+0.31m AHD as AHD +0.31m artificial closing sandbar of the proved unsatisfactory.

Four removeable stop boards floodgates to fitted raise to water levels in winter-spring to

winter flooding.

Timber floodgates upgraded, were and sill the was further lowered to -0.45mreduce to AHD

was also ocean. diverted the to

Vasse River ocean.flow the Flow to from Iron Gully, Stone Buayanyup and Cardanup Rivers

Vasse River Diversion Drain constructed divert Sabina Upper to the and virtually all of the

Extensive drainage networks input place.

Cut wasCut drain made to River ocean. the water fromto New

restrict salt water intrusion.

Timber floodgates installed exit to channels Vasse of the and Wonnerup Estuaries to

Capel river ocean diverted the to via Higgins cut.

Modification actions Modification

History of anthropogenic modification History modification and of management anthropogenic

Year

2004

1998

1997

1990

1988

1964

1948

1928

1927

1915

1908

1880

1980s

1920s

2000-2007

Table Table A1: hydrological and environmental and hydrological

Fig. A1. Past and future mean global sea level rise. For the past, proxy data are shown in light purple and tide gauge data in blue. For the future, the IPCC projections for very high emissions (red, representative concentration pathway; RCP8.5 scenario) and very low emissions (blue, RCP2.6 scenario) are shown (IPCC, 2013).

Fig. A2: The fish gate entrance prior to the installation of the PIT antenna on the downstream side of the Vasse Surge Barrier (in February 2017). N.B. the high density of barnacles (circled) on the structure known to be a food source for A. butcheri, and the school of Amniataba caudivittata.