Murray Cod (Maccullochella Peelii) Movement in the Chowilla Region of the Lower River Murray

Murray cod (Maccullochella peelii) movement in the Chowilla region of the lower River Murray

J. Fredberg, B. P. Zampatti and C. M. Bice

SARDI Publication No. F2019/000313-1 SARDI Research Report Series No. 1035

SARDI Aquatics Sciences PO Box 120 Henley Beach SA 5022

October 2019

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Murray cod (Maccullochella peelii) movement in the Chowilla region of the lower River Murray

J. Fredberg, B. P. Zampatti and C. M. Bice

SARDI Publication No. F2019/000313-1 SARDI Research Report Series No. 1035

October 2019

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

This publication may be cited as: Fredberg, J., Zampatti, B.P. and Bice, C.M. (2019). Murray cod (Maccullochella peelii) movement in the Chowilla region of the lower River Murray. South Australian Research and Development Institute (Aquatic Sciences), Adelaide. SARDI Publication F2019/000313-1. SARDI Research Report Series No. 1035. 27pp.

South Australian Research and Development Institute SARDI Aquatic Sciences 2 Hamra Avenue West Beach SA 5024 Telephone: (08) 8207 5400 Facsimile: (08) 8207 5415 http://www.pir.sa.gov.au/research

DISCLAIMER SARDI Aquatic Sciences and the Department of Environment, Water and Natural Resources (DEWNR), do not guarantee that the publication is without flaw of any kind or is wholly appropriate for you particular purposes and therefore disclaim all liability for any error, loss or other consequence which may arise from you relying on any information in this publication. The contents of this publication do not purport to represent the position of the Commonwealth of Australia or the MDBA in any way and, as appropriate, are presented for the purpose of informing and stimulating discussion for improved management of the Basin's natural resources. To the extent permitted by law, the copyright holders (including its employees and consultants) exclude all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this report (in part or in whole) and any information or material contained in it. The authors warrant that they have taken all reasonable care in producing this report. The report has been through the SARDI internal review process, and has been formally approved for release by the Research Chief, Aquatic Sciences. Although all reasonable efforts have been made to ensure quality, SARDI does not warrant that the information in this report is free from errors or omissions. SARDI and its employees do not warrant or make any representation regarding the use, or results of the use, of the information contained herein as regards to its correctness, accuracy, reliability and currency or otherwise. SARDI and its employees expressly disclaim all liability or responsibility to any person using the information or advice. Use of the information and data contained in this report is at the user’s sole risk. If users rely on the information they are responsible for ensuring by independent verification its accuracy, currency or completeness. The SARDI Report Series is an Administrative Report Series which has not been reviewed outside the department and is not considered peer-reviewed literature. Material presented in these Administrative Reports may later be published in formal peer-reviewed scientific literature. © 2018 SARDI & MDBA With the exception of the Commonwealth Coat of Arms, the Murray-Darling Basin Authority logo and photographs, all material presented in this document is provided under a Creative Commons Attribution 4.0 Australia licence (http://creativecommons.org/licences/by/4.0/). For the avoidance of any doubt, this licence only applies to the material set out in this document. The details of the licence are available on the Creative Commons website (accessible using the links provided) as is the full legal code for the CC BY 4.0 AU licence ((http://creativecommons.org/licences/by/4.0/legal code).

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SARDI Publication No. F2019/000313-1 SARDI Research Report Series No. 1035

Author(s): J. Fredberg, B.P. Zampatti and C.M. Bice Reviewer(s): Leigh Thwaites (SARDI) and J. Whittle (DEWNR) Approved by: A/Prof Q. Ye Science Leader – Inland Waters & Catchment Ecology

Signed: Date: 8th October 2019 Distribution: DEWNR, SAASC Library, Parliamentary Library, State Library and National Library Circulation: Public Domain

iii

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

TABLE OF CONTENTS

TABLE OF CONTENTS ...... iv LIST OF FIGURES ...... v LIST OF TABLES ...... v ACKNOWLEDGEMENTS ...... vii EXECUTIVE SUMMARY ...... 1 INTRODUCTION ...... 4 METHODS ...... 6 Study Site ...... 6 Radio-tagged Murray cod and ATS logger tracking ...... 8 Data Analysis ...... 12

RESULTS ...... 14 Hydrology and Regulator operations during study period ...... 14 Reach-scale habitat use and movement ...... 15 Sexual differentiation in movement ...... 19 Movement of Murray cod in relation to regulator operation ...... 21

DISCUSSION ...... 23 CONCLUSIONS AND RECOMMENDATIONS ...... 25 REFERENCES...... 26

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

LIST OF FIGURES Figure 1. Map of the Chowilla Anabranch system in the lower River Murray, South Australia. Closed red circles depict the Chowilla Creek regulator and Lock and Weir No. 6, and closed green circles depict the nine radio receiver/logger towers used to track Murray cod movement throughout Chowilla. (1 = Chowilla Creek, 2 = Boat Creek, 3 = Pipeclay Creek, 4 = Slaney Creek, 5 = Salt Creek, 6 = Swiftys Creek and 7 = Punkah Creek)...... 7 Figure 2. Mean (+SE) frequency (%) of tagged fish detected on each logger in the Chowilla system in 2013–2018...... 16 Figure 3. Mean (+SE) number of loggers visited by tagged fish per/month in the Chowilla system in 2013-2018. Red = summer, Orange = autumn, Blue = winter and Green = spring...... 18 Figure 4. Mean (+SE) number of loggers visited by tagged male and female fish between 2013-2018 in the Chowilla array system. Red = summer, Orange = autumn, Blue = winter and Green = spring...... 20 Figure 5. Mean (+SE) number of upstream and downstream movements by tagged fish between August to December (2014-2017) between; a) Murray to Regulator loggers, b) Regulator to Boat loggers and c) Murray to Boat loggers. No regulator operations occurred in 2017. n = number of individual tagged fish that were detected...... 21 Figure 6. Mean (+SE) number of detections on the Chowilla Regulator logger between August to December (2014-2017). No regulator operations occurred in 2017. n = number of individual tagged fish that were detected...... 22

LIST OF TABLES Table 1. Original capture date and location, sex, total length (mm), weight (g) and number of days detected of 69 radio-tagged Murray cod tracked via ATS loggers from July 2013 to October 2018...... 10 Table 2. PERMANOVA results comparing the mean frequency of fish detected on each logger/site between years from 2013–2018. Significant P values are highlighted in bold...... 15 Table 3. PERMANOVA results comparing the total number of loggers visited by tagged fish within months and between years from 2013–2018. Significant P values are highlighted in bold...... 17

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Table 4. PERMANOVA results comparing activity (number of loggers visited/month) between months and sexes from 2013–2018. Significant P values are highlighted in bold...... 19 Table 5. PERMANOVA pair-wise comparisons of monthly activity between sexes from 2013-2018. Significant values are highlighted in bold (B-Y corrected α = 0.016). ... 19 Table 6. PERMANOVA results comparing movement type (e.g. Murray to regulator, Regulator to Boat and Murray to Boat) between years (August to December: 2014- 2017). Significant P values are highlighted in bold...... 22

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

ACKNOWLEDGEMENTS

Thanks to the SARDI staff who assisted with fieldwork relating to this project; namely, Ian Magraith, Phillipa Wilson, Neil Wellman, Paul Jennings, Arron Strawbridge and Sandra Leigh.

Robbie Bonner, Tim Kruger, Warren Beer and Tony Waye (SA Water) provided accommodation at Lock 6 and generous hospitality. Also, thanks to Phil Strachan and Alison Stokes (DEW) for facilitating access to various parts of the Chowilla Game Reserve.

Thanks to Leigh Thwaites (SARDI) and Jan Whittle (DEW) who constructively reviewed a draft of this report. Funding for the 2018 intervention monitoring was provided by the Murray-Darling Basin Authority’s (MDBA) The Living Murray Initiative through the Department for Environment and Water, and the project was managed by Jan Whittle.

vii

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

EXECUTIVE SUMMARY

The Chowilla anabranch system, which bypasses Lock 6 on the River Murray, consists of a range of aquatic habitats including permanent lotic (flowing water) creeks, habitats which are now uncommon in the South Australian section of the lower River Murray. These lotic habitats are crucial in maintaining remnant populations of riverine fauna, including Murray cod (Maccullochella peelii), which have declined in the main-channel weir pool habitats of the lower River Murray. In 2014, the Chowilla Creek regulator and ancillary structures were constructed, with the objective of using large-scale engineered floodplain inundation to maintain or improve ‘floodplain condition’. Operation of these structures poses several ecological risks, including: 1) altering riverine hydraulics (e.g. reduced water velocities) and 2) fragmenting habitats in the Chowilla system. These have been highlighted as potential threats to Murray cod in the region through influencing habitat use and impeding movement through Chowilla Creek.

To gain understanding of the movement and habitat use of Murray cod in Chowilla, and the adjacent River Murray, since 2007, a total of 88 Murray cod have been implanted with radio-tags and a network of nine radio-receiver/logger towers, located on major tributaries of Chowilla Creek, the River Murray and the Chowilla regulator, were used to remotely collect movement data.

The objective of the current project was to explore the utility of this remotely collected data to characterise reach-scale habitat use and movement activity of Murray cod. We used data collected from 69 Murray cod between 2013–2018, as this period encompassed variable River Murray flow, regulator operation and digitally accessible remotely collected data. Specifically, we aimed to investigate:

1. Reach-scale Murray cod habitat use and movement activity over a range of years and hydrological scenarios; and 2. Movement activity of Murray cod in lower Chowilla Creek in years with and without regulator operation.

Over 2013–2018, 69 Murray cod had active radio tags. Habitat use was spatio-temporally variable, and the proportion of tagged fish detected was consistently greatest, across all years, at the Slaney Creek (16–22%), Salt Creek (6–24%) and Boat Creek loggers (14–

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

19%), indicating an affinity for habitats in these reaches. This result is consistent with contemporary understanding of Murray cod ecology, with these reaches of the Chowilla anabranch system exhibiting physical habitat (abundant woody habitat) and hydraulic characteristics (e.g. water velocities >0.3 m.s-1) preferred by Murray cod.

Activity of tagged fish (i.e. the mean number of loggers visited by tagged fish per month) was typically lowest in summer (December-February), with modest increases through autumn, and peak activity from late winter to the end of spring (August–November). Peak activity coincided with the Murray cod spawning period in the lower River Murray. Female Murray cod exhibited greater movement activity than male Murray cod, particularly between late autumn and the end of spring. Female Murray cod have previously been shown to remain active throughout the spawning season, covering larger cumulative distances than males, potentially in search of multiple mates. Alternatively, males are likely to be more sedentary and move over smaller ranges after establishing a spawning site, mating and remaining to care for eggs and larvae prior to dispersal.

In years of regulator operation (2014–2016), movements between the Murray and Regulator loggers, and between the Regulator and Boat Creek loggers, were more common than direct movements between the Murray and Boat Creek loggers. In 2017, when the regulator was not in operation, the number of movements was similar among these movement types. Additionally, the mean number of individual detections on the regulator logger was greater (≥100 detections per fish) during years with regulator operations than when the regulator was not in operation (~9 detections per fish), indicating that fish spent more time in the vicinity of the regulator when it was in operation. These results suggest that during operation of the regulator, the movement of individuals between the River Murray and core lotic habitats upstream of Boat Creek is impeded, resulting in individuals making multiple attempts to do so, and migratory delay in the vicinity of the regulator.

The results of the current study reinforce the habitat specificity of Murray cod and the importance of movement between distinct habitats in the Chowilla anabranch system. Since 2014, the Chowilla regulator has been operated annually (with the exception of 2017) over a period that incorporates Murray cod spawning and high mobility. As such, mitigation options may need to be considered (e.g. timing and frequency of regulator use) to minimise habitat fragmentation and support the maintenance of Murray cod populations in the region. Using remote logging infrastructure alone was useful in achieving the 2

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla objectives of this study, but these data may lack the spatial and temporal resolution to investigate questions regarding responses to specific interventions and altered behaviour. As such, we suggest the following recommendations to address these knowledge gaps and gain further understanding of Murray cod movement and ecology in the Chowilla region;

• Increasing the population of tagged fish and further manual tracking in association with passively collected (logger) data. This would improve the statistical power and rigour of experimental investigations regarding fish movement and behaviour in response to management intervention at Chowilla. • Investigating entrance hydraulics and attraction efficiency at the Chowilla Regulator vertical-slot fishway. Few Murray cod have used the fishway, despite being detected at the regulator, suggesting attraction efficiency may be poor. These investigations could include manipulating discharge through the Chowilla Regulator, when in operation, and visually assessing entrance hydraulics.

Keywords: Chowilla, Murray cod, movement, regulator operation

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

INTRODUCTION

The Chowilla floodplain is the largest remaining area of undeveloped floodplain in the lower River Murray (O'Malley and Sheldon 1990). Due to the construction of Lock 6, the Chowilla Anabranch system (hereafter Chowilla) exhibits permanent lotic (flowing water) habitats in what previously would have been ephemeral streams. Lotic habitats are now uncommon in the South Australian section of the River Murray, as the construction of locks and weirs has transformed the river into a series of cascading weir-pools that, under low flows (i.e. <10,000 ML.day-1), are predominantly lentic (still water) in character (Walker 2006). Flowing water habitats in Chowilla maintain remnant populations of endangered riverine fauna, including Murray cod (Maccullochella peelii), that have declined in the main-channel weir pool habitats of the lower River Murray.

In 2014, the Chowilla Creek regulator and ancillary structures were constructed, with the objective of using large-scale engineered floodplain inundation to maintain or improve ‘floodplain condition’. Operation of the regulator poses several ecological risks, including: 1) altering riverine hydraulics (e.g. reduced water velocities) to the detriment of lotic biota, such as Murray cod; and 2) fragmentation of habitats. Ultimately, operation of the regulator may impact the habitat use and population dynamics of Murray cod in the Chowilla region (Mallen-Cooper et al. 2011, Koehn et al. 2014).

From 2007–2018, SARDI Aquatic Sciences has used radio-telemetry to investigate the movement and habitat use of 88 Murray cod in Chowilla and the adjacent River Murray. As a component of this research, a network of nine radio-receiver/logger towers, located on major tributaries of Chowilla Creek, the River Murray and the Chowilla regulator, have been used to remotely collect movement data. Prior studies of Murray cod movement and habitat use at Chowilla have used a combination of data from active manual tracking and remote loggers (Leigh and Zampatti 2013, Fredberg and Zampatti 2018), including specific investigations of movement and habitat use during managed inundation events in 2014 (SARDI unpublished data) and 2016 (Fredberg and Zampatti 2018). Both studies found that the Chowilla regulator significantly altered the hydraulic characteristics of Murray cod habitats and impeded the movement of Murray cod in Chowilla Creek.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

The objective of the current project was to explore the utility of remotely collected data alone to characterise reach-scale habitat use and movement activity of Murray cod. We used data collected from 2013–2018, as this period encompassed high and low River Murray flows, regulator operation and digitally accessible remotely collected data. Specifically, we aimed to investigate:

1. Reach-scale Murray cod habitat use and movement activity over a range of years and hydrological scenarios; and 2. Movement of Murray cod in lower Chowilla Creek in years with and without regulator operation.

These tasks are fundamental to improving confidence in risk mitigation and management of the Chowilla regulator and broadening knowledge of the ecology of Murray cod in the region.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

METHODS Study Site

The Chowilla Anabranch and Floodplain system (Chowilla) is comprised of a series of anabranching creeks, backwaters, wetlands and terminal lakes that bypass Lock 6 on the River Murray, South Australia (Figure 1). Chowilla is part of the Riverland Ramsar site, a Wetland of International Importance for nationally threatened species, habitats and communities, and is considered an Icon Site under the Murray-Darling Basin Authority’s The Living Murray Program (MDBA 2016).

The Chowilla Regulator was first operated in 2014, raising water levels in Chowilla Creek from the typical 16.5 m AHD (Australian Height Datum) to 19.14 m AHD. This mid-level testing operation was followed by low level (17.85 m AHD) and high level (19.78 m AHD) operations in 2015 and 2016, respectively, though the operation in 2016 was curtailed in mid-November as a natural flood event occurred. The regulator was not operated in 2017.

In order to investigate habitat use and movement of radio-tagged Murray cod in Chowilla, a network of nine remote radio logger towers has been established at key creek junctions, enabling the remote tracking of radio-tagged fish throughout Chowilla and the adjacent River Murray (Figure 1). Despite water levels being raised in Chowilla during managed inundations, fish transitioning between different reaches of the system must still pass through key creek junctions within the detection range of logging stations.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Figure 1. Map of the Chowilla Anabranch system in the lower River Murray, South Australia. Closed red circles depict the Chowilla Creek regulator and Lock and Weir No. 6, and closed green circles depict the nine radio receiver/logger towers used to track Murray cod movement throughout Chowilla. (1 = Chowilla Creek, 2 = Boat Creek, 3 = Pipeclay Creek, 4 = Slaney Creek, 5 = Salt Creek, 6 = Swiftys Creek and 7 = Punkah Creek). 7

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Radio-tagged Murray cod and ATS logger tracking

As part of investigations regarding the habitat use and movement of Murray cod in the Chowilla region, radio-transmitters have been implanted into Murray cod across multiple tagging events from 2007–2016, (Leigh and Zampatti 2011, Wilson et al. 2015, Wilson et al. 2016, Fredberg and Zampatti 2018). For the purposes of this investigation, we used data collected from 2013–2018 from 69 Murray cod with ‘active’ tags. These fish were originally tagged between October 2007 and December 2016 (Table 1).

Radio transmitters implanted into Murray cod were cylindrical 150 MHz, internal transmitters with a 30 cm long (0.7 mm diameter) trailing antenna (Advanced Telemetry Systems (ATS), Insanti, MN, USA). Three sizes of transmitter were used: models F1850, F1855 and F1860, weighing 25, 87 and 150 g in air and having warranted battery lives of 560, 1657 and 3937 days, respectively. Transmitters were fitted with a mortality circuit that activated and produced a distinct signal if the fish (i.e. transmitter) did not move for a period of ≥8 hours. Each radio-tagged fish was also implanted with a passive integrated transponder (PIT) tag (Texas Instruments RI-TRP-REHP half-duplex eco-line glass transponders, 23.1 mm long, 3.85 mm in diameter and weighing 0.6 g in air) to facilitate detection of these fish in fishways fitted with PIT tag readers on the Chowilla Creek regulator and main channel Locks and Weirs of the River Murray (Barrett and Mallen-Cooper 2006). Plastic tipped dart tags (PDA or PDS, Hallprint, Victor Harbour, SA, Australia) were used to enable external visual identification of radio-tagged fish and reporting of captures by anglers.

Fish were captured throughout Chowilla and in the adjacent River Murray main channel using a Smith-Root® 5.0 KVA boat mounted electrofishing unit. Following capture, Murray cod were anaesthetised using 1.5 ml of AQUI-S® (Aqui-s, Lower Hutt, New Zealand) per 50 L of river water. Length and weight were recorded and fish were inverted onto a v-shaped cradle. The gills were irrigated throughout the surgery with a 50 % dilute solution of AQUI- S. An incision of 3–4 cm was made through the ventral wall slightly dorsal to the mid-ventral line beginning adjacent the pelvic fin and extending towards the anus. Where possible, the sex of the fish was determined and the transmitter inserted into the abdominal cavity. To ensure fish buoyancy was not compromised transmitter weight was ≤2 % of total body mass.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

A shielded-needle technique (Adams et al. 1998) was used to guide the trailing antenna through the lateral body wall posterior to the incision. The incision was closed with two internal and three external sutures. A long-term (2 weeks) antibiotic Baytril® (Bayer Australia, Pymble, NSW, Australia) at a dose of 0.1 mL kg-1 was then injected in the dorsal musculature. A PIT tag was inserted in the dorsal musculature forward of the dorsal fin or, in large fish, in the cheek muscle, and a dart tag was positioned between the dorsal pterygiophores. Following recovery, fish were released at their capture location.

Nine remote logging stations (ATS radio receiver/loggers model No. RC4500C) were located on key creek junctions throughout Chowilla (2007 onwards), at the junction of Chowilla Creek and the River Murray (2007 onwards), and on the Chowilla Creek regulator (2014) (Figure 1). Most stations incorporate three Yagi antennas: one facing upstream, one downstream and one in the direction of the tributary. The Chowilla Regulator logging station has two antennas, one facing upstream and one downstream Chowilla Creek. The presence of fish in the vicinity (detection range ≤600 m) of an antenna was recorded automatically as a frequency, antenna number, time and signal strength. Directionality of movement is determined based on antenna number and relative signal strength. These data were remotely transmitted to a central database. PIT tagging enabled radio-tagged fish to be detected by PIT tag readers installed in vertical-slot fishways on the Chowilla Creek regulator and those that had exited Chowilla to be detected by PIT tag readers installed in vertical-slot fishways on River Murray locks and weirs (Barrett and Mallen-Cooper 2006). Any fish moving upstream or downstream in the River Murray were identified by interrogating PIT tag reader records from fishways at the Chowilla Creek regulator and Locks No. 1–10.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Table 1. Original capture date and location, sex, total length (mm), weight (g) and number of days detected of 69 radio-tagged Murray cod tracked via ATS loggers from July 2013 to October 2018.

Date Length at Weight at No. of days Fish Number Location Sex Tagged capture (mm) capture (g) detected Slaney Creek 310m D/S Salt 150.302 (24) 23/10/2007 Unknown 810 9000 312 Creek logger River Murray opposite Chowilla 150.284.(22) 23/10/2007 Male 1010 23000 2 Creek 150.302 (23) 24/10/2007 Little Slaney Creek Male 750 8500 327

150.302 (19) 1/04/2008 Slaney Creek opposite billabong Unknown 910 12700 14 Slaney Creek ~700m U/S 150.483 (24) 1/04/2008 Male 975 19000 197 Chowilla Creek junction 150.362 (24) 2/04/2008 Slaney Creek Female 790 8500 1580

150.302 (20) 4/04/2008 River Murray (Lock 6) Male 695 5000 1

150.503.25 4/04/2008 River Murray (Lock 6) Female 995 18000 5 River Murray opposite Chowilla 150.284 (24) 8/04/2008 Female 1040 21000 176 Creek Chowilla Creek near Slaney 150.503 (24) 10/04/2008 Female 1050 21000 1397 Creek 150.342 (24) 10/04/2008 Slaney Creek Male 815 11000 394

150.362 (25) 27/11/2008 Chowilla Creek U/S Pipeclay Male 890 14290 156 Salt Creek U/S Little Slaney 150.362 (21) 20/01/2009 Unknown 1150 26500 104 Creek junction 150.342 (25) 20/01/2009 Little Slaney Creek Male 640 4500 1

150.483 (25) 20/01/2009 Little Slaney Creek junction Male 1230 30000 1109 Chowilla Creek ~400m u/s Boat 150.481(50) 5/12/2012 Unknown 583 3400 93 Creek Junction River Murray ~1300m U/S 150.502 (54) 14/05/2013 Male 1005 18200 86 Chowilla Creek River Murray U/S Chowilla 150.521 (53) 14/05/2013 Female 885 16000 49 woolshed U/S Boat Creek (Chowilla Creek 150.362 (53) 15/05/2013 Female 825 13000 211 condition monitoring site) 150.502 (50) 15/05/2013 Below Boat Creek logger tower Female 514 2058 410

150.302 (52) 16/05/2013 Lower Slaney Creek Male 955 16200 96

150.521 (52) 16/05/2013 Slaney Creek (mid) Male 970 22500 108 Lower Slaney Creek ~100m U/S 150.542 (52) 16/05/2013 Female 910 16500 360 Chowilla junction 150.542 (55) 16/05/2013 Slaney Creek (mid) Female 820 11000 11

150.521 (55) 17/05/2013 Chowilla Creek D/S Boat Creek Female 920 13500 1100 Slaney Creek ~750m D/S 150.302 (50) 21/05/2013 Immature 485 1395 42 billabong Slaney Creek ~800m D/S 150.481 (51) 21/05/2013 Male 581 3623 96 billabong Slaney Creek immediately 150.481 (54) 21/05/2013 Male 1180 33000 191 outside billabong Island opposite Pipeclay Creek 150.502 (51) 21/05/2013 Immature 454 1379 291 junction 150.342 (54) 22/05/2013 Rivre Murray U/S Millewa Female 630 4340 27

150.342 (53) 4/06/2013 Little Slaney Creek Male 1100 29000 716

150.502 (52) 4/06/2013 Slaney Creek U/S billabong Unknown 1230 38000 34

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Table 1 cont. Original capture date and location, sex, total length (mm), weight (g) and number of days detected of 69 radio-tagged Murray cod tracked via ATS loggers from July 2013 to October 2018.

Length at No. of days Weight at Fish Number Date Tagged Location Sex capture detected capture (g) (mm) Slaney Creek at Punkah Island 150.481 (53) 4/06/2013 Male 1180 37000 631 launch Slaney Creek at Punkah Island 150.542 (56) 4/06/2013 Female 1170 31000 537 launch River Murray immediately 150.302 (54) 2/12/2013 Male 675 4930 99 opposite Chowilla Junction River Murray ~1km us 150.362 (52) 2/12/2013 Female 1080 22000 478 Murray/Chowilla Junction 150.302 (53) 3/12/2013 Chowilla Creek 400m U/S bridge Male 920 13000 67

150.502 (53) 3/12/2013 Salt Creek Male 1120 26000 4

150.521 (56) 3/12/2013 Salt Creek Female 1140 25500 1 Slaney Creek ~ 1500m u/s 150.342 (51) 5/12/2013 Unknown 450 1300 120 Chowilla Creek 150.481 (52) 5/12/2013 Slaney Creek D/S old island Male 1190 32000 240 Chowilla Creek U/S of Boat 150.481 (56) 5/12/2013 Unknown 583 3400 1 Creek 150.521 (59) 5/12/2013 Slaney/Chowilla Creek junction Male 770 10000 559

150.542 (53) 6/12/2013 Chowilla Creek U/S Boat Creek Female 1010 20000 160

150.361 (59) 17/05/2016 Chowilla Creek U/S Hancock Ck Male 800 9100 131 Chowilla Creek ~ 100m U/S Boat 150.362 (50) 17/05/2016 Male 622 3400 670 Creek 150.521 (58) 17/05/2016 Chowilla Creek U/S Boat Creek Female 775 5800 25

150.542 (59) 17/05/2016 Slaney Creek logger Male 718 7100 230 Slaney Creek ~ 800m U/S 150.301 (58) 18/05/2016 Female 1090 20500 137 gauging station Slaney Creek condition 150.302 (51) 18/05/2016 Male 620 3900 27 monitoring site 150.361 (58) 18/05/2016 Slaney Creek entrance Female 816 7800 144 Slaney Creek U/S condition 150.362 (51) 18/05/2016 Male 579 3200 14 monitoring site 150.481 (57) 18/05/2016 Slaney Creek (lower) Male 1200 32000 81

150.481 (58) 18/05/2016 Slaney Creek (mid) Female 782 10900 62 Slaney Creek ~ 800m U/S 150.502 (56) 18/05/2016 Immature 473 2100 16 gauging station Slaney Creek condition 150.521 (54) 18/05/2016 Female 772 7700 379 monitoring site 150.502 (58) 19/05/2016 Chowilla Creek D/S Bridge Male 980 18000 294

150.301 (59) 24/05/2016 Slaney Creek at Billabong Male 920 15000 45

150.341 (58) 24/05/2016 Slaney Creek at Billabong Male 1050 21000 16 Slaney Creek at Salt Creek 150.342 (52) 24/05/2016 Female 650 4500 174 Junction 150.361 (57) 24/05/2016 Little Slaney Creek (upper) Female 1060 23500 277 Slaney Creek ~300m D/S 150.502 (57) 24/05/2016 Male 658 5000 27 Billabong 150.502 (59) 24/05/2016 Slaney Creek just D/S Billabong Male 1190 34500 90 Slaney Creek D/S Salt Creek 150.542 (54) 24/05/2016 Female 950 16500 37 Junction 150.542 (57) 24/05/2016 Little Slaney Creek (mid) Female 920 13000 266 Salt Creek ~ 500m U/S Slaney 150.341 (57) 26/05/2016 Male 1210 36000 14 Logger Salt Creek 1.5km D/S Swifty's 150.542 (58) 26/05/2016 Female 1080 23000 105 Creek 150.502 (55) 26/05/2016 Bank K Female 540 2900 47

150.361 (56) 27/05/2016 River Murray D/S Lock 6 Male 515 2800 22

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Data Analysis

Reach-scale habitat use and movement

Habitat use and movement of radio-tagged Murray cod within the Chowilla region was investigated by assessing affinity to specific remote loggers (receivers) and movement activity between remote loggers. Affinity was defined as the percentage of active fish detected on each remote logger per month within each year over 2013–2018. Over the same period, activity was defined as the number of different remote loggers each radio-tagged fish was detected upon per month.

Spatio-temporal variability in affinity and activity were investigated using two-factor uni- variate PERMANOVA (permutational ANOVA) (Anderson and Ter Braak 2003) performed on Euclidean Distance similarity matrices in the package PRIMER v. 6.1.12 and PERMANOVA+ (Anderson et al. 2008). For affinity, factors were logger site and year, and the sampling unit was percentage of tagged fish detected on each logger per month. These data were arcsine transformed prior to analyses as raw data were proportions. For activity, factors were month and year, and sampling unit was the number of receivers visited for each unique fish. The same analyses were performed to investigate differences in seasonal movement activity between male and female fish. A significance level of α = 0.05 was adopted for all main tests and when pairwise comparisons were required, the B-Y method significance correction was applied (α = 0.016) (Benjamini and Yekutieli 2001). For analyses of sex-based differences in activity, p-values were generated using the Monte Carlo (randomisation) technique due to low numbers of unique permutations.

Movement through lower Chowilla Creek

Upstream and downstream movements undertaken by radio-tagged fish between the Murray, Regulator and Boat Creek loggers were characterised as one of the following movement types; a) between the Murray and Regulator loggers; b) between the Regulator and Boat Creek loggers; and c) between the Murray and Boat Creek loggers. The influence of the Chowilla Regulator on the movement of Murray cod in lower Chowilla Creek was assessed by comparing the frequency of movement ‘types’ (defined above) and frequency of detection on the regulator logger (a proxy for time spent in the vicinity of the regulator) during months associated with regulator operations (operating range: 10 August – 18 December), among years. A two-factor uni-variate PERMANOVA, performed on Euclidean

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Distance similarity matrices was used to investigate differences in the frequency of movements among defined movement types (e.g. Murray to regulator, Regulator to Boat Creek and Murray to Boat Creek) and years of regulator operation and no operation. Additionally, a single-factor uni-variate PERMANOVA performed on Euclidean Distance similarity matrices was used to investigate differences in the mean number of detections (per fish) on the Chowilla regulator logger among years.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

RESULTS

Hydrology and Regulator operations during study period From July 2013 to October 2018, flow in Chowilla Creek and the adjacent River Murray was variable. Between July 2013 and July 2016, hydrology in the River Murray at the South Australian border (QSA) was characterised by low flows (<7,500 ML.d-1), punctuated by small to medium within-channel flows (up to ~25,000 ML.d-1). Over this period, flows in the River Murray and Chowilla Creek ranged 2,528–25,841 ML.d-1 and 1,351–8,910 ML.d-1, respectively. In mid-July 2016, flow in the River Murray steadily increased with high flows peaking in late November/early December at 94,565 ML.d-1. This event was associated with extensive overbank flooding and an anoxic blackwater event in the southern MDB, including the Chowilla region. By January 2017, flows had receded to <20,000 ML.d-1 and decreased to a minimum of 2,798 ML.d-1 in winter 2018, before increasing again to a peak of 17,642 ML.d-1 in October 2018. Over this period, flow in Chowilla Creek ranged 1,567–5,167 ML.d-1.

In 2014, the Chowilla Regulator was operated from 5 September–5 December, with upstream water levels peaking at 19.14 m AHD in mid-October. In 2015, the regulator was operated 6 October to 18 December, with upstream water levels peaking at 17.85 AHD in mid-November. In 2016, the regulator was operated from 10 August–17 November, with upstream water levels peaking at 19.78 m AHD late September. Regulator operations in both 2014 and 2016 were also in conjunction with water level raising at Lock 6, whereby upstream peak water levels reached 19.6 AHD in late October and 19.8 AHD in early October, respectively. The regulator was not operated in 2017.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Reach-scale habitat use and movement All 69 fish were detected on logging stations over the study period with the number of detection days ranging 1–1580, and >50% of individuals were detected on ≥100 days. Two-factor PERMANOVA performed on affinity data indicated a significant interaction between the factors ‘year’ and ‘site/logger’ (Table 2), suggesting that spatial habitat use was not consistent among years. The mean frequency of tagged fish detected on the remote loggers in Chowilla varied annually (Figure 2), but in all years, the percentage of tagged fish detected was typically greatest at the Slaney Creek (16–22%), Salt Creek (6– 24%) and Boat Creek loggers (14–19%). The percentage of fish at the Pipeclay and Swifty’s loggers were more variable, but was greatest in 2014–2017 (12–14%). In all years, fish were absent or detected in only low percentages (≤3%) at the Punkah and Bank K loggers, whilst consistently low percentages (3–7%) of tagged fish were detected annually on loggers in lower Chowilla Creek (i.e. Murray and Regulator loggers) (Figure 2).

Table 2. PERMANOVA results comparing the mean frequency of fish detected on each logger/site between years from 2013–2018. Significant P values are highlighted in bold.

Factor df Pseudo-F P Year 5, 575 10.836 0.001 Site 8, 575 67.783 0.001 Year x Site 40, 575 2.2429 0.001

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

30 30

2013 2016 25 25

20 20

15 15

10 10

5 5

0 0

SE) 30 30 + 2014 2017 25 25

20 20

15 15

10 10

5 5

0 0 30 30 Mean frequency (%) of tagged fish ( of tagged (%) frequency Mean

2015 2018 25 25

20 20

15 15

10 10

5 5

0 0

Boat Salt Boat Salt Murray Slaney Swiftys Bank K Murray Slaney Swiftys Bank K Pipeclay Punkah Pipeclay Punkah Regulator Regulator

Figure 2. Mean (+SE) frequency (%) of tagged fish detected on each logger in the Chowilla system in 2013–2018.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Two-factor PERMANOVA, performed on activity data (number of loggers visited per month), indicated a significant difference between months and years, with no interaction (Table 3). This suggests the activity of tagged fish varied among years, but the differences among months were consistent across years. General patterns were characterised by lowest activity in summer (December–February), with modest increases over the three months of autumn and peak activity from August–November (Figure 3).

Table 3. PERMANOVA results comparing the total number of loggers visited by tagged fish within months and between years from 2013–2018. Significant P values are highlighted in bold.

Factor df Pseudo-F P Month 11, 2799 24.471 0.001 Year 5, 2799 2.8266 0.018 Month x Year 47, 2799 1.3504 0.054

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

1.8 1.8

1.6 2013 1.6 2016

1.4 1.4

1.2 1.2

1.0 1.0

0.8 0.8

0.6 0.6

0.4 0.4

0.2 0.2

0.0 0.0

1.8 1.8 2014 SE) 1.6 1.6 2017 +

1.4 1.4

1.2 1.2

1.0 1.0

0.8 0.8

0.6 0.6

0.4 0.4

0.2 0.2 Mean no. of loggers visited ( visited no. of Mean loggers 0.0 0.0

1.8 1.8

1.6 2015 1.6 2018

1.4 1.4

1.2 1.2

1.0 1.0

0.8 0.8

0.6 0.6

0.4 0.4

0.2 0.2

0.0 0.0 July July May May April April June June March March August August October January January October February February November December November December September September

Figure 3. Mean (+SE) number of loggers visited by tagged fish per/month in the Chowilla system in 2013-2018. Red = summer, Orange = autumn, Blue = winter and Green = spring.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Sexual differentiation in movement Two-factor PERMANOVA indicated a significant interaction between fish sex and month (Table 4), suggesting differences in the activity of the sexes were not consistent among months. Seasonal patterns in activity, with limited activity from January–April and greatest activity from May–December, were similar for both sexes (Figure 4). Pair-wise comparisons revealed that activity was similar for both sexes from January–April, but was significantly greater for female fish during the months of May–December (B-Y corrected α = 0.016) (Table 5).

Table 4. PERMANOVA results comparing activity (number of loggers visited/month) between months and sexes from 2013–2018. Significant P values are highlighted in bold. Factor df Pseudo-F P Sex 1, 2502 102 0.001 Month 11, 2502 24.043 0.001 Sex x Month 11, 2502 1.9454 0.031

Table 5. PERMANOVA pair-wise comparisons of monthly activity between sexes from 2013-2018. Significant values are highlighted in bold (B-Y corrected α = 0.016).

Pairwise Comparison Month Sex Sex t P (MC) January Male Female 1.8133 0.072 February Male Female 1.0853 0.290 March Male Female 1.5581 0.143 April Male Female 1.6376 0.107 May Male Female 4.26 0.001 June Male Female 4.5756 0.001 July Male Female 3.7271 0.001 August Male Female 2.6833 0.005 September Male Female 4.2437 0.001 October Male Female 3.4257 0.001 November Male Female 2.9351 0.006 December Male Female 2.804 0.006

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

2.0

1.8 Male (n = 33) Female (n = 26) 1.6

1.4

1.2

1.0

0.8

0.6

0.4 Mean no. of loggers visted (+SE) visted no. of Mean loggers 0.2

0.0 July May April June March August January October February November December September

Figure 4. Mean (+SE) number of loggers visited by tagged male and female fish between 2013-2018 in the Chowilla array system. Red = summer, Orange = autumn, Blue = winter and Green = spring.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Movement of Murray cod in relation to regulator operation In years of regulator operation (2014–2016), the mean number of direct upstream and downstream movements undertaken by individual Murray cod between the Murray and Boat Creek loggers were lower than between the Murray and Regulator loggers, and the Boat Creek and Regulator loggers (Figure 5). Alternatively, in 2017, the mean number of movements undertaken by individual Murray cod was comparable for all three movement types. Nonetheless, these differences were not statistically significant by year or movement type (Table 6), potentially due to high variability in the numbers of movements made by individual fish and low sample sizes (Figure 5).

12 Murray to Regulator SE)

+ Regulator to Boat 10 (n = 4) Murray to Boat

(n = 3) 8

(n = 4) 6

(n = 4) (n = 3) 4 (n = 5) (n = 5) (n = 5) (n = 3) 2 (n = 3) (n = 4) (n = 2) Meanno. of movements by tagged fish ( 0 2014 2015 2016 2017

Figure 5. Mean (+SE) number of upstream and downstream movements by tagged fish between August to December (2014-2017) between; a) Murray to Regulator loggers, b) Regulator to Boat loggers and c) Murray to Boat loggers. No regulator operations occurred in 2017. n = number of individual tagged fish that were detected.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Table 6. PERMANOVA results comparing movement type (e.g. Murray to regulator, Regulator to Boat and Murray to Boat) between years (August to December: 2014-2017). Significant P values are highlighted in bold.

Factor df Pseudo-F P Movement Type 2, 68 0.8369 0.413 Year 3, 68 0.5834 0.613 Movement Type x Year 6, 68 0.8142 0.569

During years of regulator operation (2014–2016), the mean number of individual detections on the Regulator logger (≥100 detections per fish) were greater than during 2017 (~9 detections per fish), when the regulator was not operated (Figure 6). These differences, however, were not statistically significant (Pseudo-F3, 33 = 0.57378, p = 0.672), potentially due to high variability between individuals (during years of regulator operation) and low sample sizes (Figure 6).

200

175 (n = 8) (n = 13)

(n = 6)

SE) 150 +

125

100

50 Mean no. of ( Mean detections

25 (n = 7)

0 2014 2015 2016 2017

Figure 6. Mean (+SE) number of detections on the Chowilla Regulator logger between August to December (2014-2017). No regulator operations occurred in 2017. n = number of individual tagged fish that were detected.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

DISCUSSION To improve knowledge of the spatial ecology of Murray cod and aid management of the Chowilla Regulator, we investigated the reach-scale habitat use and movement of radio- tagged Murray cod using data collected from remote logging stations. Specifically, using data collected over the period 2013–2018, which comprised variable hydrology and years with and without regulator operation, we explored: 1) reach-scale patterns of Murray cod habitat use (affinity) and movement activity within Chowilla, and 2) the influence of regulator operation on specific movements in lower Chowilla Creek.

Habitat use and activity

Whilst there was inter-annual variability in the numbers of unique fish detected on individual loggers, the highest proportions of tagged fish were consistently detected on loggers in Slaney Creek (i.e. Slaney and Salt loggers) and in Chowilla Creek adjacent Boat Creek. These reaches of the system also comprise the majority of original capture, tagging and release locations. High detection rates indicate affinity to these regions, which are characterised by a combination of abundant instream wood (snags) and lotic habitats (i.e. flowing water). This result is consistent with previous research on Murray cod habitat use at Chowilla (SARDI unpublished data; Fredberg and Zampatti 2018) and other regions of the River Murray (Koehn and Nicol 2014), which have suggested an association with hydraulically complex flowing water (e.g. water velocities >0.3 m s-1) and snags. In regions where instream wood is less abundant and/or stream hydraulics less favourable (e.g. lower water velocities), proportions of fish detected on remote loggers were low. Nevertheless, most of these regions constitute important thoroughfares for Murray cod movement within Chowilla or between Chowilla and the River Murray

The activity of Murray cod, measured as the number of distinct loggers visited by fish per month, was least during the summer months and greatest between late winter and the end of spring, a period that coincides with Murray cod reproduction in the lower River Murray (Zampatti et al. 2011, Fredberg and Zampatti 2018). During this period, females exhibited greater activity than males. Male Murray cod establish a spawning site, potentially in late winter, and after mating with a female, care for the eggs and larvae until dispersal (Lintermans 2007). Hence, males are likely to be more sedentary and move over small ranges whilst caring for a brood (Fredberg and Zampatti 2018). In contrast, females do not share parental care and may remain active after spawning whilst potentially searching for another mate (Rourke et al. 2009). 23

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

Movement and regulator operation

Lower Chowilla Creek is the primary movement corridor for reproductively mature Murray cod transitioning between the River Murray and the structurally complex, lotic habitats of Chowilla (Leigh and Zampatti 2013, Fredberg and Zampatti 2018). Access to these unique habitats in Chowilla is considered important for sustaining the integrity of Murray cod populations in this region (Zampatti et al. 2014). In 2014–2016, during regulator operations, the mean number of movements characterised as a transition between the regulator and the next upstream (Boat) or downstream (Murray) logger, were greater than direct movements along Chowilla Creek between the River Murray and core habitats upstream of Boat Creek, while with no regulator in place, the mean number of movements appeared similar among these different movement types. In addition, the mean number of detections of fish on the regulator logger were greater during years of regulator operation. Differences in the frequency of movement types and detections between regulator scenarios, however, were not statistically significant, most likely due to small sample sizes. Nevertheless, these patterns suggest that in the presence of the regulator, individuals were impeded in moving between the Murray and Boat Creek loggers, resulting in multiple attempts to do so, and increased time spent in the vicinity of the regulator. We propose these results do indeed reflect the influence of the regulator on fish movement, and generally concur with previous studies that indicate operation of the Chowilla regulator impedes the movement of Murray cod along Chowilla Creek during the reproductive season (Fredberg and Zampatti 2018; SARDI unpublished). Fishways are one means of mitigating this impact, but use of the regulator vertical-slot fishway by Murray cod has been minimal (Fredberg and Zampatti 2018). As such, alternative mitigation options (e.g. timing and frequency of regulator use) and a precautionary approach to site management to minimise habitat fragmentation and sustain Murray cod populations in the region could be considered.

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

CONCLUSIONS AND RECOMMENDATIONS Movement amongst habitat patches is integral to the persistence of riverine fish populations (Dexter et al. 2014). In the lower River Murray, Chowilla provides unique structural and hydraulic habitats that contribute to the maintenance of a significant regional population of Murray cod (Zampatti et al. 2014). The results of the current study reinforce the habitat specificity of Murray cod and the importance of movement between distinct habitats. In concert with previous investigations, there was a distinct seasonal and sex-related aspect to movement behaviour of Murray cod in the Chowilla region, indicating these behaviours are related to reproduction. Consequently, connectivity and the maintenance of specific habitats is likely fundamental to Murray cod population persistence in this region. Operations of the Chowilla Regulator that avoid seasonal periods of elevated movement activity (i.e. September–November) are likely to have the least impact on the Murray cod population.

This study employed the unique approach of solely using passively collected detection data to explore questions pertaining to the spatial ecology of Murray cod in Chowilla. Whilst these data appear appropriate for describing spatial patterns in activity and movement, they may lack the spatial and temporal resolution to answer questions regarding behavioural responses to specific interventions and altered behaviour. As such, we suggest the following recommendations to address these knowledge gaps and gain further understanding of Murray cod movement and ecology in the Chowilla region;

Fredberg, J. et al. (2019) Murray cod Movement in Chowilla

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