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Lower Murray-Darling Catchment Action Plan: Fish Community Monitoring Report Card for the 2011/12 Reporting Period

Authors:
Fisheries NSW
– Fisheries Research Report Series:
Lower Murray-Darling Catchment Action Plan:
Fish Community Monitoring
Report Card for the 2011/12 reporting period.
by
Dean Gilligan
June 2013
ISSN 1837-2120
32
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Fisheries Research in New South Wales
Fisheries research activities in the NSW Department of Primary Industries are based at various centres throughout
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Fisheries Management Act, 1994.
Title:
Lower Murray-Darling Catchment Action Plan: Fish Community Monitoring Report Card
for the 2011/12 reporting period.
Authors:
Dean Gilligan
Published By:
NSW Department of Primary Industries
Postal Address:
Port Stephens Fisheries Institute
Taylors Beach Road,
Taylors Beach,
NSW 2316
Internet:
0Hwww.dpi.nsw.gov.au
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ISSN 1837-2120
Note: Prior to July 2004, this report series was published by NSW Fisheries as the ‘NSW Fisheries Resource
Assessment Report Series’ with ISSN number 1440-057X. Then, following the formation of the NSW Department of
Primary Industries the report series was published as the ‘NSW Department of Primary Industries – Fisheries
Final Report Series’ with ISSN number 1449-9959.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 i
TABLE OF CONTENTS
1HTABLE OF CONTENTS.................................................................................................................................86HI
2HLIST OF TABLES 87HII
3HLIST OF FIGURES ....................................................................................................................................... 88HII
4HACKNOWLEDGEMENTS............................................................................................................................89HV
5HNON-TECHNICAL SUMMARY................................................................................................................90HVI
6HINTRODUCTION 91H9
7HMETHODS 92H11
8HSampling 93H11
9HData analysis.................................................................................................................................. 94H15
10HSTATUS OF INDIVIDUAL FISH SPECIES ............................................................................................. 95H18
11HSUSTAINABLE RIVERS AUDIT FISH ASSEMBLAGE CONDTION INDICATORS AND
OVERALL CONDITION INDEX ...................................................................................................
96H32
12HExpectedness Indicator................................................................................................................... 97H32
13HRecruitment Indicator..................................................................................................................... 98H33
14HNativeness Indicator....................................................................................................................... 99H35
15HOverall fish condition..................................................................................................................... 100H38
16HOTHER FISH ASSEMBLAGE PARAMETERS USEFUL FOR UNDERSTANDING THE
‘HEALTH’ OF FISH COMMUNITIES..........................................................................................
101H41
17HSpecies richness.............................................................................................................................. 102H41
18HTotal abundance............................................................................................................................. 103H41
19HTotal biomass ................................................................................................................................. 104H44
20HProportion of total catch suffering from a health condition .......................................................... 105H46
21HPROGRESS TOWARD THE LOWER MURRAY-DARLING CATCHMENT ACTION PLAN FISH
‘NATIVENESS’ TARGETS FOR RIVERINE HEALTH.............................................................
106H48
22HNative:alien species ratio............................................................................................................... 107H48
23HNative:alien abundance ratio......................................................................................................... 108H49
24HNative:alien biomass ratio ............................................................................................................. 109H49
25HTHREATENED FISH RE-INTRODUCTIONS......................................................................................... 110H58
26HDISCUSSION 111H59
27HREFERENCES 112H63
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
ii Fisheries Research Report Series: No. 32
LIST OF TABLES
28HTable 1. Primary and secondary sites sampled within each of five catchment zones in the Lower Murray-
Darling CMA catchment area...............................................................................................................
113H12
29HTable 2. Tertiary (floodplain wetland) sites associated with primary and secondary riverine sites within
each of four riverine catchment zones sampled during the 2011/12 reporting period..........................
114H13
30HTable 3. Additional sites to monitor the survival of captive bred endangered fish (southern pygmy perch
and olive perchlet) reintroduced into the Lower Murray-Darling CMA catchment area on 6 May 2011.
115H13
31HTable 4. Size limits used to distinguish new recruits for each species............................................................116H15
32HTable 5. The proportional change in the average abundance of each species at those sites where it has been
recorded……........................................................................................................................................
117H18
33HTable 6. Meta-analysis output of trends in the abundance of each species across the full time series of data
since the fish assemblages of the CMA area were benchmarked in 2004............................................
118H19
34HTable 7. Fish assemblages collected at Washpen Creek and Thegoa Lagoon < 1 year after the release of
~4,500 southern pygmy perch at Washpen Creek and ~4,500 southern pygmy perch and 700 olive
perchlet at Thegoa Lagoon on 6 May 2011..........................................................................................
119H58
LIST OF FIGURES
35HFigure 1. Flow data from gauging stations within the Lower Murray-Darling CMA area spanning the period
over which the CMA’s fish monitoring program has collected fish assemblage data..........................
120H10
36HFigure 2. The locations of primary and secondary fish survey sites and targeted threatened species
monitoring sites sampled in the 2012 season........................................................................................
121H14
37HFigure 3. The proportion of sites across the Lower Murray-Darling CMA area where each species was
collected during each sampling round..................................................................................................
122H20
38HFigure 4. Distribution, abundance and recruitment of common carp (Cyprinus carpio). ..............................123H21
39HFigure 5. Distribution, abundance and recruitment of bony herring (Nematalosa erebi). .............................124H22
40HFigure 6. Distribution, abundance and recruitment of golden perch (Macquaria ambigua)..........................125H22
41HFigure 7. Distribution, abundance and recruitment of Murray cod (Maccullochella peelii)..........................126H23
42HFigure 8. Distribution, abundance and recruitment of goldfish (Carassius auratus).....................................127H23
43HFigure 9. Distribution, abundance and recruitment of freshwater catfish (Tandanus tandanus – endangered
population). .......................................................................................................................................
128H24
44HFigure 10. Distribution, abundance and recruitment of silver perch (Bidyanus bidyanus – vulnerable)........129H24
45HFigure 11. Distribution, abundance and recruitment of redfin perch (Perca fluviatilis).................................130H25
46HFigure 12. Distribution, abundance and recruitment of spangled perch (Leiopotherapon unicolor)..............131H25
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 iii
47HFigure 13. Distribution, abundance and recruitment of Australian smelt (Retropinna semoni)..................... 132H26
48HFigure 14. Distribution, abundance and recruitment of carp-gudgeon species complex (Hypseleotris spp). 133H26
49HFigure 15. Distribution, abundance and recruitment of Murray-Darling rainbowfish (Melanotaenia
fluviatilis)…..
134H27
50HFigure 16. Distribution, abundance and recruitment of eastern mosquitofish (Gambusia holbrooki)........... 135H27
51HFigure 17. Distribution, abundance and recruitment of unspecked hardyhead
(Craterocephalus stercusmuscarum fulvus).........................................................................................
136H28
52HFigure 18. Distribution, abundance and recruitment of flat-headed gudgeon (Philypnodon grandiceps). .... 137H28
53HFigure 19. Distribution, abundance and recruitment of Oriental weatherloach (Misgurnus
anguillicaudatus)…... ..........................................................................................................................
138H29
54HFigure 20. Distribution, abundance and recruitment of dwarf flat-headed gudgeon
(Philypnodon macrostomus)................................................................................................................
139H29
55HFigure 21. Distribution, abundance and recruitment of Murray hardyhead (Craterocephalus fluviatilis
critically endangered)...........................................................................................................................
140H30
56HFigure 22. Distribution, abundance and recruitment of southern pygmy perch (Nannoperca australis
endangered)..........................................................................................................................................
141H30
57HFigure 23. Distribution, abundance and recruitment of olive perchlet (Ambassis agassizii –endangered).... 142H31
58HFigure 24. Annual change in the average expectedness indicator (SR-FIe) across the Lower Murray-Darling
CMA area between 2004 and 2012......................................................................................................
143H33
59HFigure 25. Native fish recruitment metrics representing 1) the average proportion of sites at which each
native fish is recruiting, 2) the proportion of native fish recruiting somewhere within each zone and 3)
the average proportion of abundance of each native species that are new recruits .............................
144H34
60HFigure 26. Annual change in the average recruitment indicator (SR-FIr) across the Lower Murray-Darling
CMA area between 2004 and 2012......................................................................................................
145H35
61HFigure 27. Proportion of total fish biomass that is made up by native species in the Lower Murray-Darling
river system in 2012.............................................................................................................................
146H36
62HFigure 28. Proportion of total fish abundance that is made up of native species in the Lower Murray-Darling
river system in 2012.............................................................................................................................
147H37
63HFigure 29. Proportion of total fish species richness that are native species in the Lower Murray-Darling river
system in 2012. ....................................................................................................................................
148H38
64HFigure 30. Annual change in the average nativeness indicator (SR-FIn) across the Lower Murray-Darling
CMA area between 2004 and 2012......................................................................................................
149H39
65HFigure 31. Annual change in the average fish condition index (SRA ndxFS) across the Lower Murray-
Darling CMA area between 2004 and 2012.........................................................................................
150H39
66HFigure 32. Annual changes in the average fish condition index (SRA ndxFS), expectedness (SR-FIe),
recruitment (SR-FIr) and nativeness (SR-FIn) indicators within each Lower Murray-Darling CMA
management zone between 2004 and 2012..........................................................................................
151H40
67HFigure 33. Total species richness for fish in the Lower Murray-Darling river system in 2012...................... 152H42
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
iv Fisheries Research Report Series: No. 32
68HFigure 34. Average (± SE) total species richness of native and alien fishes in each CMA management zone
and the overall Lower Murray-Darling CMA area between 2004 and 2012........................................
153H42
69HFigure 35. Total abundance of fish in the Lower Murray-Darling river system in 2012................................154H43
70HFigure 36. Average total abundance of native and alien fishes in each CMA management zone and the
overall Lower Murray-Darling CMA area between 2004 and 2012.....................................................
155H43
71HFigure 37. Total biomass of fish in the Lower Murray-Darling river system in 2012....................................156H45
72HFigure 38. Average total biomass of native (above) and alien (below) fishes in the each cma management
zone and the overall Lower Murray-Darling CMA area between 2004 and 2012.. .............................
157H45
73HFigure 39. The percentage of individuals affected by the range of symptoms of disease or parasites recorded
within the CMA area between 2004 and 2012. ....................................................................................
158H46
74HFigure 40. Proportion of total fish catch that is suffering from a health condition in the Lower Murray-
Darling river system… .........................................................................................................................
159H47
75HFigure 41. The percentage of individuals of each species affected by symptoms of disease or parasites
recorded within the cma area between 2004 and 2012.........................................................................
160H47
76HFigure 42. Comparison of the median native:alien species ratio observed in 2006, 2007, 2009, 2010, 2011
and 2012 with the benchmark (2004) and target (55% improvement) ratios. ......................................
161H50
77HFigure 43. Comparison of the median native:alien abundance ratio observed in 2006, 2007, 2009, 2010,
2011 and 2012 with the benchmark (2004) and target (25% improvement) ratios. .............................
162H50
78HFigure 44. Comparison of the median native:alien biomass ratio observed in 2006, 2007, 2009, 2010, 2011
and 2012 with the benchmark (2004) and target (25% improvement) ratios. ......................................
163H51
79HFigure 45. Progress towards the cap target of a 55% improvement in the ratio of native:alien species as at
2012…………......................................................................................................................................
164H53
80HFigure 46. Progress towards the cap target of a 25% improvement in the ratio of abundance of native:alien
species as at 2012. ................................................................................................................................
165H54
81HFigure 47. Progress towards the cap target of a 25% improvement in the ratio of biomass of native:alien
species as at 2012. ................................................................................................................................
166H55
82HFigure 48. Overall progress towards the Lower Murray-Darling CMA cap riverine health targets for
native:alien fish as at 2012. ..................................................................................................................
167H56
83HFigure 49. The proportion of sites in each progress category in each year of sampling since the Lower
Murray-Darling CMA commenced monitoring progress towards CAP targets (after benchmarking
native:alien fish ratios across the cma area in 2004). ...........................................................................
168H57
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 v
ACKNOWLEDGEMENTS
Funds for this project were supplied by the Lower Murray-Darling CMA and Fisheries NSW. Jake
Coulton, Marty Hill, Sean Lethlean, Duncan McLay, Tim McGarry, Prue McGuffie, Craig Mercier,
Justin Stanger and John Stuart undertook the fieldwork and sampling for the 2011/12 reporting
period. Thanks go to Wayne Robinson, Terry Hillman and Frederick Bouckaert from the Murray-
Darling Basin Authority’s Sustainable Rivers Audit team for advice on calculation of the fish
metrics and to Steve Carter from Environmental Dynamics for providing the ‘Fish Expert Rules’
systems software and guiding me through its implementation. Staff from the Lower Murray-
Darling CMA are thanked for arranging the loan of the CMAs Trimble unit and GPS camera,
helping set up the Trimble and providing comments on an earlier draft of this report. Bob Creese,
Kelly Fyfe, Craig Mercier, Leigh Pyke and Troy Muster provided valuable comments on draft
versions of this report. This research was undertaken under the NSW Fisheries Animal Care and
Ethics Committee approval number 98/14.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
vi Fisheries Research Report Series: No. 32
NON-TECHNICAL SUMMARY
Lower Murray-Darling Catchment Action Plan: Fish Community Monitoring Report Card
for the 2011/12 reporting period.
PRINCIPAL INVESTIGATOR: Dr Dean Gilligan
ADDRESS: Fisheries NSW
Batemans Bay Fisheries Centre
Braysyth Building
Cnr of Beach Road and Orient Street
Batemans Bay, NSW 2536
OBJECTIVES:
1. Determination of the progress toward the LMD Riverine Health Catchment Target in relation
to improvements in the native to introduced fish ratio (55% improvement in species ratio, 25%
improvement in abundance ratio, 25% improvement in biomass ratio).
2. Determination and analysis of trends in fish species & communities throughout the LMD
catchment in terms of species richness, total abundance, total biomass, proportion native
species, proportion native abundance, proportion native biomass, proportion recruits and
proportion with a health condition.
The Lower-Murray-Darling Catchment Action Plan (CAP) identifies Riverine Health as a
Catchment Target: An identifiable net improvement in riverine health across the Lower Murray-
Darling Catchment by 2015. The CAP states that this will be determined by:
an improvement in the native to introduced fish ratio (55% improvement in species ratio,
25% improvement in abundance ratio, 25% improvement in biomass ratio);
a 20% reduction in the number of days subject to blue green algal alerts; and
the reinstatement of more natural flow patterns as modelled in each of five river
management zones.
This annual summary reports on progress towards the fish community catchment targets up until
the end of the 2011/12 financial year. Fish assemblages were benchmarked across five reporting
zones within the Lower Murray-Darling CMA area in 2004 (Gilligan 2005) and have been
monitored in all but one year since 2006 (no monitoring was undertaken in 2008). This report
reports on all data collected up until 2012 to gauge progress towards the CAP targets. In 2012, fish
sampling was undertaken at 44 sites between 22 February and 3 August as part of the monitoring
program, with additional samples collected at two threatened species release sites; Washpen Creek
and Thegoa Lagoon.
The CAP target of a 55% improvement in the native:alien species ratio was not met in any
catchment zone in 2012. An annual decrease in the native:alien species ratio was statistically
significant in the Lakes CMA management zone over the 2011/12 reporting period, but not in any
other CMA management zone or across the catchment overall. As at 2012, the native:alien species
ratio was improving at 30% of monitoring sites but continued to decline at 61% of sites, with all
zones in poorer condition than they were when benchmarked in 2004 and the overall CMA
condition in 2012 being significantly lower than the benchmark condition, having declined by 15%
of the benchmark value. Across the entire CMA area, the proportion of sites occupied by each alien
species has increased from an average of 30% in 2004 to 39% in 2012 while the proportion of sites
occupied by each native species has declined from an average of 40% in 2004 to 29% in 2012.
2010/11 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 vii
The CAP target of a 25% improvement in the native:alien abundance ratio was not met in any
catchment zone in 2012. Despite significant improvements in the native:alien abundance ratios in
both the upper Murray River and lower Murray River CMA management zones between 2011 and
2012, the overall trend during the CAP reporting period between 2004 and 2012 has been a
statistically significant decrease in the native:alien abundance ratio. Despite achieving the CAP
target for the native:alien abundance ratio at 16% of individual sites in 2012, the CAP target of a
25% improvement was not achieved across any CMA zone, with all zones in poorer condition than
they were in 2004 and the overall CMA condition declining by 30% of the benchmark value. The
average abundance of native fish has declined by 60% from an average of 214 ± 42 in 2004 to 85 ±
17 in 2012. Despite a major decrease in the abundance of alien fish recorded since 2011, the
average abundance of alien fish is still 229% higher than it was in 2004, increasing from a average
of 21 ± 4 individuals per site when benchmarked in 2004 to 48 ± 14 individuals in 2012. The net
result of the declining abundance of native fishes and the increasing abundance of alien fishes since
2004 is a CMA wide decline in the native:alien abundance ratio.
In contrast to the species diversity and abundance ratios, which were declining across all catchment
zones, the CAP target of a 25% improvement in the native:alien biomass ratio target was achieved
within the lower Murray River zone downstream of the Darling River junction. However, the result
did not register as a statistically significant change given the high variability between sites (the
CAP target was exceeded at three of the seven sites but progress was poor or extremely poor at the
remaining four). The target improvement was not reached within any other CMA management
zone, which were all in poorer condition than they were in 2004. The overall trend during the CAP
reporting period between 2004 and 2012 has been a statistically significant decrease in the
native:alien abundance ratio, with overall condition declining by 76% of the benchmark value
despite the CAP target being exceeded at 25% of individual sites in 2012. The average biomass of
native fish has declined by 65% from an average of 10.9 ± 1.9 kg per sample in 2004 to 3.8 ± 0.8
kg in 2012. Alien fish biomass also declined across the CMA area, but only by 37% of the
benchmark value, decreasing from 20.9 ± 6.3 kg per sample in 2004 to 13.3 ± 2.7 kg in 2012. The
net result is a CMA wide decline in the native:alien biomass ratio since 2004.
To provide a broader perspective on the condition of fish assemblages within the CMA area and
trends in condition through time, the SRA analytical framework has been applied to the entire 2004
- 2012 time series of data collected for the CMA’s fish monitoring program. This provides a more
comprehensive assessment of fish community health than had been possible previously as it
incorporates assessment of three indicators reflecting distinct aspects of the ‘health’ of fish
communities: Expectedness, Recruitment and Nativeness, rather than just indicators of aspects of
Nativeness alone, and provides a method to aggregate these indicators into an overall Fish
Condition Index. The Expectedness Indicator represents the proportion of native species that are
found within a CMA management zone compared to the number historically present, the
Recruitment Indicator represents the recent reproductive activity of the native fish community and
the Nativeness Indicator represents the proportion of native versus alien fishes (and is most similar
to the CMA’s existing CAP targets for native:alien ratios). After aggregating the Expectedness,
Recruitment and Nativeness Indicators, the SRA Fish Condition Index characterised fish
assemblages as in ‘Poor Condition’ when benchmarked across the CMA area in 2004. Fish
assemblages remained poor (or even declined slightly) through until 2010, when Recruitment and
to a lesser extent Expectedness improved as a result of moderate flooding in the Darling River and
downstream reaches in early 2010. However, decreases in Recruitment and Nativeness in 2011
(associated with widespread major flooding and a subsequent protracted hypoxic blackwater
event), and further decreases in Recruitment and Expectedness in 2012 (associated with a second
major widespread flood event), have resulted in current fish assemblages being rated in ‘Very Poor
Condition’ across the CMA area. The overall trend between 2004 and 2012 has been a significant
decline in overall fish condition, with the condition of fish assemblages in 2012 the lowest that it
has been since fish monitoring commenced in the CMA area. As at 2012, current fish condition is
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
viii Fisheries Research Report Series: No. 32
‘Extremely Poor’ in the Lakes (ndx FS = 13 ± 2) and Darling River (14 ± 1) CMA management
zones, ‘Very Poor’ in the Great Darling Anabranch (22 ± 2), Upper Murray River (23 ± 2) and
lower Murray River (33 ± 2), and ‘Poor’ in floodplain wetlands (41 ± 3).
Notable positive changes in the abundance of individual species occurring between 2011 and 2012
sampling events were:
The collection of catfish in the lower Murray River zone and Coonpour Creek for the first time
in 2012.
Declines in the abundance of goldfish across most zones (with none detected in the upper
Murray River zone).
A ~90% decline in the abundance of carp following the 2011 recruitment boom (with carp now
only 2.5 times more abundant in 2012 than they were in 2004 – down from 21 times more
abundant in 2011)
Notable negative changes in the abundance of individual species occurring between 2011 and 2012
sampling events were:
A decline in abundance of silver perch in the upper Murray River zone.
The virtual disappearance of the formerly common unspecked hardyhead from the Murray River
and its floodplain wetlands.
The anticipated decline or disappearance of spangled perch from many of the sites they
colonised during the 2010 and 2011 floods.
Little improvement in the abundance of Murray cod after declines observed following the
hypoxic blackwater flow event in the Murray River in 2011and continuation of the decline in
Murray cod abundance observed in the Darling River since 2006.
An 87% decline in the abundance of golden perch following the 2011 recruitment boom (with
golden perch now only 80% of their abundance in 2004).
Very large declines in the abundance of Murray-Darling rainbowfish across all CMA zones.
A 76% decline in the abundance of bony herring following the 2010 and 2011 recruitment
boom (with bony herring now only 62% of their abundance in 2004).
The continued low abundance of Australian smelt in the upper Murray River zone and decline
in abundance in the Darling River.
The proportion of fish affected by a health condition continued to increase across most CMA
zones between 2011 and 2012.
Neither olive perchlet or southern pygmy perch, the two threatened fishes reintroduced into
Thegoa Lagoon or Washpen Creek in May 2011 were recaptured at the release sites or any other
monitoring sites during sampling in 2012.
Together, these data suggest that the management actions implemented to June 2012 have not been
sufficient to result in much progress towards achieving the three Lower Murray-Darling CMA CAP
targets for fish community ‘nativeness’, at a level where the CAP targets are likely to be met across
the CMA area by 2015. The same recommended management actions suggested in previous years
still apply in 2012:
1. Implementing carp control programs.
2. Threatened species recovery actions.
3. Promoting the maintenance of large stable populations of large adult Murray cod, golden
perch, silver perch and freshwater catfish within the CMA area.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No.32 9
INTRODUCTION
The Lower-Murray-Darling Catchment Action Plan (CAP) identifies Riverine Health as a
Catchment Target: An identifiable improvement in riverine health across the Lower Murray-
Darling Catchment by 2015. The CAP states that this will be determined by:
an improvement in the native to introduced fish ratio (55% improvement in species ratio,
25% improvement in abundance ratio, 25% improvement in biomass ratio);
a 20% reduction in the number of days subject to blue green algal alerts; and
the reinstatement of more natural flow patterns as modelled in each of five river
management zones.
This annual summary reports on progress towards the fish community catchment targets within the
catchment area, including rivers, lakes and wetlands, with riverine sites stratified within five pre-
determined catchment management zones (Figure 1):
1. Lakes (Menindee Lakes, Lake Victoria and Euston Lakes).
2. Darling River.
3. Great Darling Anabranch.
4. Murray River upstream of the Darling junction (Murray I).
5. Murray River downstream of the Darling junction (Murray II).
And a sixth additional category:
6. Floodplain wetlands (combined across zones 2 – 5 above).
The objectives of the fish monitoring program are:
1. Determination of the progress toward the LMD Riverine Health Catchment Target in
relation to improvements in the native to introduced fish ratio (55% improvement in
species ratio, 25% improvement in abundance ratio, 25% improvement in biomass ratio).
2. Determination and analysis of trends in fish species & communities throughout the LMD
catchment in terms of species richness, total abundance, total biomass, proportion native
species, proportion native abundance, proportion native biomass, proportion recruits and
proportion with a health condition.
The fish community was benchmarked at a number of sites established and sampled in 2004
(Gilligan 2005). Progress up until 2006, 2007, 2009, 2010 and 2011 were reported in Gilligan
(2007), Gilligan (2008), Gilligan (2009), Gilligan (2010) and Gilligan (2012) respectively. This
document reports on progress up until 2012.
For the second consecutive year the catchment area experienced a major natural disturbance during
the 2011/12 CMA reporting period, with major flooding occurring across the CMA’s entire
network of aquatic ecosystems. The 2011/12 flood peak in the Darling River and flows delivered to
the Great Darling Anabranch were very similar in timing, amplitude and duration to the 2010/11
event (Figure 1). In contrast, the 2011/12 flooding in the Murray River peaked approximately two
months later than the preceding 2010/11 flood and was both less protracted and of lower amplitude
(Figure 1). Importantly, flooding in the Murray River in 2011/12 did not result in as significant
hypoxic blackwater flows as had occurred the previous year (Whitworth et al. 2011).
The 2011/12 data adds to what is becoming an increasingly valuable dataset for interpreting the
response of fish to drought, floods, hypoxic blackwater events and other associated disturbances
(Figure 1).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
10 Fisheries Research Report Series: No .32
Figure 1. Flow data from gauging stations within the Lower Murray-Darling CMA area spanning the period over which the CMAs fish monitoring
program has collected fish assemblage data (data provided by the MDBA). Blue shaded columns represent sampling periods within which fish
assemblage data were collected (and excludes SRA sampling periods). Black shaded columns approximate periods where each CMA
management zone was reported to be affected by hypoxic blackwater (< 4 mg/L dissolved oxygen) (modified from Whitworth et al. 2011).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No.32 11
METHODS
Sampling
The sampling procedure used was identical to that used for the benchmarking surveys undertaken
in 2004 and described in Gilligan (2005) and is consistent with that used for the Murray-Darling
Basin Authority’s Sustainable Rivers Audit (Davies et al. 2010). In the 2012 season, sampling in
the Menindee Lakes, Great Darling Anabranch and upper sections of the Darling River was
delayed by several months because of floodwaters and road closures. The first sample was
collected on 22 February 2012, but sampling could not be completed in heavily flood affected areas
until 3 August. Most samples were collected under high flow conditions. The exceptions were;
Nangiloc, Boston Bend and upper Kulnine in the Murray River and Grand Junction and the Darling
Anabranch mouth in the Great Darling Anabranch which were sampled just before or as
floodwaters commenced to rise in late February – early March, and Bono on the Darling River
which could not be accessed until after floodwaters had receded in early August.
With the exception of Imperial Lake at Broken Hill, the full complement of primary and secondary
sites (Table 1 & Figure 2) and 8 of the 28 tertiary sites (Table 2) were sampled. Ongoing sampling
at Broken Hill was discontinued in 2012 as it was becoming increasingly obvious that the fish
community present within the reservoir, which was established entirely through fish stocking, was
not representative of the fish assemblages of other lakes within the CMA area and because the
increased variance was reducing the statistical power for detecting change at other sites within the
Lakes & Reservoirs zone. Only eight of the tertiary wetland sites (two wetland sites within each
CMA management zone) were sampled in 2012 due to budget constraints. Both the threatened
species release sites established in 2011; Thegoa Lagoon and Washpen Creek (Table 3 & Figure 2)
were re-sampled in order to assess survival of the captive bred olive perchlet and southern pygmy
perch released on 6 May 2011. Because these sites were not randomly selected, data was not used
in calculations as part of the fish monitoring program. However, the data were plotted in the maps
(but not the accompanying bar graphs) for individual species abundance and recruitment (Figures 4
to 23).
Pre-existing data from 2004, 2006, 2007, 2009, 2010 and 2011 were collected under the Lower
Murray-Darling CMA’s fish monitoring project. Data from 2005 and 2008 were collected for the
Murray-Darling Basin Authority’s Sustainable Rivers Audit (SRA) IP1 and IP4 sampling rounds.
Although the sampling locations for the SRA in 2005 and 2008 are not entirely consistent with
those established for the LMD CMA monitoring program, both projects used a similar random site
selection process and aim for the same site density per zone. However, only three and one SRA
sites were present in the lower Murray River zone in 2005 and 2008 respectively, as the zone
boundary for the SRA straddles the NSW-SA border, and a portion of the seven SRA sites lay
within South Australia. Therefore, SRA data for the lower Murray River zone is less
comprehensive than that from the Darling and upper Murray River zones. Further, the SRA does
not sample any locations within the Lakes zone, Great Darling Anabranch or floodplain wetlands.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
12 Fisheries Research Report Series: No .32
Table 1. Primary and secondary sites sampled within each of five catchment zones in the
Lower Murray-Darling CMA catchment area.
Site name Waterway Latitude Longitude
Murray I
Tangles Corner Murray River -34.69159 143.06219
Yungera Island Murray River -34.69187 142.96832
Carina Bend Murray River -34.67714 142.70019
Wemen Murray River -34.76543 142.64555
The Boiler Murray River -34.74963 142.50942
Nangiloc Murray River -34.48269 142.36868
Boston Bend Murray River -34.12884 142.03491
Murray II
Upper Kulnine Murray River -34.13118 141.83983
Ned’s Corner Murray River -34.12791 141.33987
Frenchman’s Creek Frenchman’s Creek -34.10051 141.39952
10 km below Lock 7 Murray River -34.07452 141.19219
Hancock Hill- Wompinni Murray River -34.04404 141.04413
Salt Creek Salt Creek -34.00286 141.04241
Tareena Salt Creek -33.96318 141.00710
Darling River
Bono Darling River -32.55987 142.39083
Moorara Darling River -33.22470 142.37290
Pooncarie Darling River -33.38246 142.56233
Lethero Darling River -33.58937 142.44700
Lelma Darling River -33.67577 142.39452
Downham Farm Darling River -33.80628 142.07518
Pomona Darling River -33.98030 141.91340
Great Darling Anabranch
Woodlands Great Darling Anabranch -33.27826 141.78891
Wycott Great Darling Anabranch -32.97873 142.05350
Cuthero Bridge Great Darling Anabranch -33.07444 142.00902
Hunter waterhole Great Darling Anabranch -33.23857 141.92631
Four Wings Shack Great Darling Anabranch -33.18811 141.99448
Grand Junction Great Darling Anabranch -34.02255 141.81836
Darling Anabranch mouth Great Darling Anabranch -34.09002 141.75970
Lakes
Lake Wetherell Menindee Lakes -32.31234 142.50727
Copi Hollow Menindee Lakes -32.26773 142.38109
Lake Pamamaroo Menindee Lakes -32.28276 142.42591
Lake Menindee Menindee Lakes -32.28489 142.34975
Lake Cawndilla Menindee Lakes -32.45032 142.26356
Lake Benanee Euston Lakes -34.54734 142.88799
Dry Lake Euston Lakes -34.52952 142.85711
Lake Victoria Lake Victoria -34.03940 141.28626
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No.32 13
Table 2. Tertiary (floodplain wetland) sites associated with primary and secondary riverine
sites within each of four riverine catchment zones in the Lower Murray-Darling CMA
catchment area that were sampled during the 2011/12 reporting period.
Wetland name (MWWG No.) Associated riverine site Latitude Longitude
Murray I
Peacock Creek (No. 1637) Yungera Island -34.66236 142.99676
Tuckers Creek (No. 294) Boston Bend -34.10112 141.99467
Murray II
Coonpoor Creek (No. 407) Ned’s Corner -34.10316 141.30657
Cliffhouse Wetland (No. 128) Hancock Hill-Wompinni -34.04930 141.04570
Darling River
Keiara Billabong Bono -32.59723 142.39035
Pomona Wetland Pomona -33.99888 141.89935
Great Darling Anabranch
Binjie Billabong Woodlands -33.29470 141.75170
Unnamed wetland Wycott -32.98000 142.06430
Table 3. Additional sites to monitor the survival of captive bred endangered fish (Southern
pygmy perch and olive perchlet) reintroduced into the Lower Murray-Darling CMA
catchment area on 6 May 2011.
Site name (MWWG No.) Waterway Latitude Longitude
Thegoa Lagoon (No. 367) Thegoa Lagoon -34.11250 141.88260
Meilman (No. 1455) Washpen Creek -34.57600 142.87400
Fisheries Research Report Series: No. 32 Page 14
Figure 2. The locations of primary and secondary fish survey sites (yellow labels) and targeted threatened species monitoring sites (blue labels) sampled
in the 2012 season. The locations of tertiary survey sites (floodplain wetlands) are presented as grey dots, but are not labelled (site details can
be obtained from Table 2).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 15
Data analysis
Metrics, Indicators and the Overall Fish Condition Index.
Metrics were derived from the raw data as per previous reports: Abundance of individual species,
the proportion of individuals of each species classified as new recruits (Table 4), total species
richness, native species richness, alien species richness, total abundance, native abundance, alien
abundance, total biomass, native biomass, alien biomass, the proportion of native species,
abundance and biomass, the ration of native: alien species, abundance and biomass and the
proportion of fish with a health condition.
Table 4. Size limits used to distinguish new recruits for each species. Values represent the length at
1 year of age for longer-lived species or the age at sexual maturity for species that
reach maturity within 1 year.
Species Estimated size at 1 year old or at sexual maturity
(Fork or Total Length)
Native species
Australian smelt 40 mm (Pusey et al. 2004)
Bony herring 67 mm (Cadwallader 1977)
Carp-gudgeon species-complex 35 mm (Pusey et al. 2004)
Dwarf flat-headed gudgeon 30 mm (Pusey et al. 2004)
Flat-headed gudgeon 58 mm (Pusey et al. 2004, Llewellyn 2007)
Unspecked hardyhead 40 mm (Pusey et al. 2004)
Freshwater catfish 83 mm (Davis 1975)
Golden perch 75 mm (Mallen-Cooper 1996)
Murray cod 235 mm (Rowland 1998)
Murray-Darling rainbowfish 45 mm (Pusey et al. 2004: for M. duboulayi)
Silver perch 75 mm (Mallen-Cooper 1996)
Spangled perch 68 mm (Leggett & Merrick 1987)
Alien species
Common carp 200 mm (Brown et al. 2003)
Eastern gambusia 21 mm (for females) (McDowall 1996)
Goldfish 100 mm (Brumley 1996)
Oriental weatherloach 76 mm (Wang et al. 2009)
Redfin perch 60 mm (maximum reported by Heibo & Magnhagen 2005)
NOTES: Data in this table reflects the average of the mean male and female lengths presented in the source
literature. Where standard length rather than total length is presented, the data were transformed to total length
using a conversion factor estimated from available preserved specimens and/or photographs of suitable quality.
Additional metrics necessary to generate the three fish condition indicators (Expectedness,
Recruitment and Nativeness) and the overall fish condition index (SRA ndxFS) used to report on
river health by the Sustainable Rivers Audit (Davies et al. 2010) were derived following the
procedures described by Robinson (2012). This was done for the complete 2004-2012 time series
of data collected under the CMA’s fish monitoring program. Metric and indicator aggregation was
done using Expert Rules analysis in the Fuzzy Logic toolbox of MatLab (The Mathworks Inc.
USA) using the rule sets developed by Davies et al. (2010).
The Expectedness Indicator (SR-FIe) represents the proportion of native species that are now found
within a CMA management zone, compared to that which was historically present. The predicted
pre-European fish community of each zone was derived using the Reference Condition for Fish
(RC-F) approach used by the Sustainable Rivers Audit program. The RC-F process involves using
available historical and contemporary data, museum collections and expert knowledge to determine
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
16 Fisheries Research Report Series: No. 32
the complete species list for each zone and estimate the probability of collecting each species at any
randomly selected site within each zone if it were sampled using the standard sampling protocol
prior to 1770 (Davies et al. 2008). Historically rare species (collected at 0 < 0.2 of samples) are
allocated an RC-F score of 0.1, occasional species (collected at 0.21 < 0.7 of samples) an RC-F of
0.45 and common species (collected at 0.71 < 1.0 samples) an RC-F of 0.85 (RC-F scores being the
median capture probability within each category). The Expectedness Indicator is derived from two
input metrics; the observed native species richness over the RC-F corrected expected species
richness at each site (O/E), and the total native species richness observed within the zone over the
total number of species predicted to have existed within the CMA management zone historically
(O/P) (Robinson 2012). The two expectedness metrics were aggregated using the Expectedness
Indicator Expert Rule set (Carter 2012).
The Recruitment Indicator (SR-FIr) represents the recent reproductive activity of the native fish
community within each CMA management zone. The Recruitment Indicator is derived from three
input metrics; the proportion of native species showing evidence of recruitment at a minimum of
one site within a zone, the average proportion of sites within a zone at which each species captured
was recruiting (RC-F corrected), and the average proportion of total abundance of each species that
are new recruits (Robinson 2012). Recruits are young fish that represent the recent breeding
activity of the population and do not necessarily meet the classical definition of recruitment to the
adult population. For this study, we assumed recruits to be fish less than one year old for larger,
long-lived species and immature individuals for smaller species that mature at less than one year of
age. Individuals were identified as recruits if they were smaller than the length cut-offs reported in
the literature as referenced in Table 4. Where species-specific data was not available, data from a
related surrogate species was used. The three recruitment metrics were aggregated using the
Recruitment Indicator Expert Rule set (Carter 2012).
The Nativeness Indicator (SR-FIn) represents the proportion of native versus alien fishes within the
river. The Nativeness Indicator is derived from three input metrics; proportion native biomass,
proportion native abundance and proportion native species (Robison 2012). The three Nativeness
metrics were aggregated using the Nativeness Indicator Expert Rule set (Carter 2012).
These three indicators were then combined using the Fish Index Expert Rule set (Carter 2012) to
calculate an overall Fish Condition Index (SRA ndxFS). The Fish Index Expert Rules analysis is
weighted as SR-FIe > SR-FIr > SR-FIn. The output generated by the Expert Rules analysis is
scaled between 0 and 100, with higher values representing a ‘healthier’ fish community.
Statistical analysis
To analyse changes occurring during the 2011/12 reporting period, each metric, indicator and the
overall fish condition index values for 2012 were compared at CMA zone and overall catchment
level with those observed in 2011 using paired t-tests. Analysis of individual species’ abundance
only utilised sites at which each species had been collected at least once within the complete time
series of data. All error bars within the text, tables and figures, excluding those relating to
native:alien ratios are standard error. Error bars for ratios equal one standard deviation.
Prior to analysis, native, alien and total abundance and biomass variables were 4
th
root transformed,
the proportion of total species, abundance and biomass that were native were arcsine transformed,
the proportion of individuals suffering a health condition were square-root transformed and the
native: alien ratio variables and abundance data for individual species were log
10
(x+1) transformed
in order to normalise the data and/or equalise the variances. Native, alien and total species richness,
SR-FIe, SR-FIr, SR-Fin and SRA ndxFS were suitable for parametric analysis without
transformation.
To analyse trends observed between 2004 (when the fish assemblages of the CMA area were
benchmarked) and 2012, non-parametric Spearmen’s rank correlation was used to test for a
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 17
relationship between each fish assemblage or individual species parameter and sampling date. Only
sites sampled on at least four occasions were included. Meta-analysis (Comprehensive Meta-
analysis version 2.2, Biostat, Englewood USA) was used to aggregate the trend data from
individual sites to test for a CMA area-wide trend and for underlying spatial heterogeneity amongst
CMA management zones. To undertake the meta-analysis, the correlation coefficient and sample
size were used to derive an effect size (Fisher’s Z) for each parameter at each site. Effect size
estimates for each parameter were then combined across the entire study area using a random
factors meta-analysis where each site represents a ‘comparison’. Meta-analysis of each species’
abundance data only utilised sites at which species had been collected at least once within the time
series of data. Meta-analysis of fish assemblage parameters used the complete set of sites. Spatial
heterogeneity across the CMA area was tested for using the Q test. If spatial heterogeneity was
significant, separate meta-analyses were run using data from each of the CMA management zones
individually in an attempt to partition the regional variability. However, meta-analysis results only
test for strength and statistical significance of the trend – not the rate of change in the parameter
being analysed.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
18 Fisheries Research Report Series: No. 32
STATUS OF INDIVIDUAL FISH SPECIES
All but four of the twenty native and alien species collected in previous rounds of sampling were
collected in 2012. The exceptions were: critically endangered Murray hardyhead (Craterocephalus
fluviatilis) which was only collected during SRA sampling at a single site (Merrinee North, Murray
River -34.15869, 141.47201) in 2005, endangered southern pygmy perch (Nannoperca australis)
which was only collected at the Washpen Creek threatened species release site (Meilman) 20 days
after release in 2011, native dwarf flat-headed gudgeon (Philypnodon macrostomus) which had
been collected at one site in 2010 and oriental weatherloach (Misgurnus anguillicaudatus), which
were recorded for the first time in the CMA area at three sites in the upper Murray River CMA
management zone in 2011. Other than the endangered freshwater catfish (Tandanus tandanus), all
other species collected have been recorded within the CMA area in every year since the fish
monitoring program commenced in 2004.
The percentage changes in abundance of each species across the CMA area during the 2011/12
reporting period are presented in Table 5. Only two species increased in abundance between 2011
and 2012 sampling events; carp-gudgeons (Hypseleotris spp) and flat-headed gudgeon
(Philypnodon grandiceps), but neither increase was statistically significant (Table 5). In contrast,
eight of the remaining 16 species (18 if reintroduced threatened species are included) had exhibited
statistically significant declines in abundance during the past year (Table 5).
Table 5. The proportional change in the average abundance of each species at those sites where
it has been recorded (across the whole catchment). Statistically significant changes in
abundance are shaded.
Species Percentage change in abundance during the 2011/12 reporting period
Carp-gudgeon species complex 267% increase (p = 0.924)
Flat-headed gudgeon 233% increase (p = 0.476)
Olive perchlet* No data
Southern pygmy perch* No data
Murray hardyhead No data
Dwarf flat-headed gudgeon No data
Murray cod 36% decrease (p = 0.371)
Australian smelt 43% decrease (p < 0.001)
Goldfish 59% decrease (p < 0.001)
Freshwater catfish 60% decrease (p = 0.719)
Silver perch 60% decrease (p = 0.171)
Bony herring 67% decrease (p = 0.736)
Redfin perch 68% decrease (p = 0.068)
Eastern mosquitofish 71% decrease (p = 0.003)
Common carp 84% decrease (p < 0.001)
Golden perch 86% decrease (p < 0.001)
Murray-Darling rainbowfish 91% decrease (p < 0.001)
Unspecked hardyhead 91% decrease (p < 0.001)
Spangled perch 97% decrease (p < 0.001)
Oriental weatherloach 100% decrease
* Threatened species reintroduced to the CMA area in 2011, but not yet detected at any of the
CMA fish monitoring program sites.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 19
Meta-analyses of trends in the abundance of individual species over the complete time-series of
data since fish assemblages were benchmarked in 2004 suggest significant changes in abundance of
11 of the 20 species sampled in or reintroduced into the CMA area during the existing CAP period
(Table 6). Of these, seven species have increased in abundance (four native and three alien species)
and four species have declined (all native) (as indicated by either positive or negative Fisher’s Z
values). There was no significant spatial heterogeneity across the CMA area for any species other
than alien redfin perch (Perca fluviatilis) (Table 6), where abundance has increased significantly in
the upper and lower Murray River CMA management zones but not in the Darling River or
floodplain wetlands. There was further spatial heterogeneity within the Lakes zone, with a
significant decline in abundance at Lake Benanee (p = 0.005) but no trend at Lake Victoria (p =
0.302).
Table 6. Meta-analysis output of trends in the abundance of each species across the full time
series of data since the fish assemblages of the CMA area were benchmarked in 2004.
Raw data were the Spearman’s rank correlation for each species at each site. N is the
number of sites at which each species had been collected at least once since 2004.
Fisher’s Z is the statistic used to test significance of the trend. Greater values represent
stronger trends and the sign of the value indicates an increasing trend (positive values)
or declining trend (negative values). The Q statistic represents heterogeneity across
samples within the meta-analysis. Statistically significant statistics are highlighted in
grey.
Species N Fisher’s Z
P Q
df
p
Common carp 33 7.207 < 0.001 27.902 32 0.674
Golden perch 31 5.042 < 0.001 18.387 30 0.952
Goldfish 32 4.822 < 0.001 36.760 31 0.219
Spangled perch 17 4.494 < 0.001 3.417 16 0.999
Silver perch 21 3.371 0.001 11.575 20 0.930
Bony herring 33 2.031 0.042 31.288 32 0.502
Freshwater catfish 4 1.904 0.057 1.172 3 0.760
Eastern mosquitofish 32 1.892 0.059 21.699 31 0.892
Redfin perch 12 1.484 0.138
20.253 11 0.042
Lower Murray River 6 2.347 0.019 5.880 5 0.318
Upper Murray River 2 1.972 0.049 0.211 1 0.646
Lakes 2 -0.500 0.617 7.863 1 0.005
Darling River 1 0 0.999
Floodplain Wetlands 1 -0.476 0.634
Oriental weatherloach 2 1.171 0.242 0.092 1 0.761
Dwarf flat-headed gudgeon 2 0.478 0.633 0.091 1 0.763
Murray hardyhead 1 -0.875 0.381
Australian smelt 33 -1.318 0.188 35.487 32 0.307
Murray-Darling rainbowfish 30 -1.711 0.087 24.191 19 0.719
Murray cod 18 -2.722 0.006 10.062 17 0.901
Flat-headed gudgeon 21 -3.276 0.001 19.208 20 0.508
Unspecked hardyhead 23 -3.809 <0.001 18.677 22 0.665
Carp-gudgeon species complex 32 -5.135 < 0.001 39.822 31 0.133
Those species that have increased in prevalence (the proportion of sites occupied) by more than
10% of sites between 2004 and 2012 were the native spangled perch (0% of sites in 2004 to 11% in
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
20 Fisheries Research Report Series: No. 32
2012) and the alien eastern mosquitofish (11% in 2004 to 33% in 2012), redfin perch (4% in 2004
to 11% in 2012) and goldfish (41% in 2004 to 52% in 2012)(Figure 3). Those species that
decreased in prevalence by more than 10% of sites were; Murray-Darling rainbowfish (63% in
2004 to 17% in 2012), flat-headed gudgeon (22% of sites in 2004 to 7% in 2012), Murray cod
(56% in 2004 to 20% in 2012), unspecked hardyhead (33% in 2004 to 13% in 2012), carp-
gudgeons (78% in 2004 to 39% in 2011) and Australian smelt (81% in 2004 to 57% in
2012)(Figure 3). In the context of the CMA’s native:alien ratio CAP targets, three of the four
species that were increasing in distribution were alien species and all six species that were
retracting in distribution were native.
0 0.2 0.4 0.6 0.8 1
Spangled perch
Eastern mosquitofish
Redfin perch
Silver perch
Freshwater catfish
Goldfish
Bony herring
Common carp
Golden perch
Australian smelt
Carp-gudgeons
Unspecked hardyhead
Murray cod
Flat-headed gudgeon
Murray-Darling
rainbowfish
Oriental weatherloach
Dwarf flat-headed
gudgeon
Proportion of total sites
2004
2006
2007
2009
2010
2011
2012
Figure 3. The proportion of sites across the Lower Murray-Darling CMA area where each
species was collected during each sampling round. Species are ranked in order of
the extent of change since 2004, with species increasing in prevalence at the top to
those decreasing in prevalence at the bottom.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 21
The following figures (Figures 4 to 23) present three types of data for each fish species known to
be present within the catchment area during the CAP reporting period (in order of greatest to least
biomass across the whole catchment); 1) the distribution and abundance of each species at each site
in 2012, 2) the distribution and abundance of recruits at each site in 2012 and 3) trends in
abundance since 2004 in each catchment zone.
1. Distribution and abundance is reflected by the locations and size of the dot (black and/or
green) at each sampling location. The size scaling of the dots varies across species and can
be gauged relative to the legend in the bottom right corner of each figure.
2. Recruits are defined as those individuals smaller than the length cut-offs presented in Table
4, which represent fish less than 1 year of age (0+) or size at sexual maturity for species
that mature rapidly. The distribution and abundance of recruits is reflected by the
distribution and size of green dots at each sampling location. The absence of a green dot at
a site means that no recruits of that species were sampled in 2012. If recruits were present,
the size of the green dot matches the abundance scale described by the legend.
3. Trends in abundance from 2004 through to 2012 are presented for each catchment zone and
for the catchment as a whole as a bar graph. The height of the bar reflects the average
abundance across all sites in that zone and the error bars represent the standard error of the
mean (non-transformed data).
Figure 4. Distribution, abundance and recruitment of common carp (Cyprinus carpio).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
22 Fisheries Research Report Series: No. 32
Figure 5. Distribution, abundance and recruitment of bony herring (Nematalosa erebi).
Figure 6. Distribution, abundance and recruitment of golden perch (Macquaria ambigua).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 23
Figure 7. Distribution, abundance and recruitment of Murray cod (Maccullochella peelii).
Figure 8. Distribution, abundance and recruitment of goldfish (Carassius auratus).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
24 Fisheries Research Report Series: No. 32
Figure 9. Distribution, abundance and recruitment of freshwater catfish (Tandanus tandanus
– Endangered population).
Figure 10. Distribution, abundance and recruitment of silver perch (Bidyanus bidyanus
Vulnerable).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 25
Figure 11. Distribution, abundance and recruitment of redfin perch (Perca fluviatilis).
Figure 12. Distribution, abundance and recruitment of spangled perch (Leiopotherapon
unicolor).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
26 Fisheries Research Report Series: No. 32
Figure 13. Distribution, abundance and recruitment of Australian smelt (Retropinna semoni).
Figure 14. Distribution, abundance and recruitment of carp-gudgeon species complex
(Hypseleotris spp).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 27
Figure 15. Distribution, abundance and recruitment of Murray-Darling rainbowfish
(Melanotaenia fluviatilis).
Figure 16. Distribution, abundance and recruitment of eastern mosquitofish (Gambusia
holbrooki).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
28 Fisheries Research Report Series: No. 32
Figure 17. Distribution, abundance and recruitment of unspecked hardyhead (Craterocephalus
stercusmuscarum fulvus).
Figure 18. Distribution, abundance and recruitment of flat-headed gudgeon (Philypnodon
grandiceps).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 29
Figure 19. Distribution, abundance and recruitment of Oriental weatherloach (Misgurnus
anguillicaudatus). Note: This species was not collected in 2012.
Figure 20. Distribution, abundance and recruitment of dwarf flat-headed gudgeon
(Philypnodon macrostomus). Note: This species was not collected in 2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
30 Fisheries Research Report Series: No. 32
Figure 21. Distribution, abundance and recruitment of Murray hardyhead (Craterocephalus
fluviatilis – critically endangered). Note: This species was not collected in 2012.
Figure 22. Distribution, abundance and recruitment of southern pygmy perch (Nannoperca
australis – endangered). Note: This species was not collected in 2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 31
Figure 23. Distribution, abundance and recruitment of olive perchlet (Ambassis agassizii
endangered). Note: This species was not collected in 2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
32 Fisheries Research Report Series: No. 32
SUSTAINABLE RIVERS AUDIT FISH ASSEMBLAGE
CONDTION INDICATORS AND OVERALL
CONDITION INDEX
The MDBA’s Sustainable Rivers Audit program (Davies et al. 2010) established a set of fish
assemblage metrics reflecting aspects of the ‘health’ of fish communities of the Murray-Darling
Basin and a method to aggregate these into themed indicators (Expectedness, Recruitment and
Nativeness) and an overall fish condition index (SRA ndxFS). In addition to being used to report
on river health within the Murray-Darling Basin, the SRA assessment approach has been applied to
all regions of NSW as part of the NSW Government’s Monitoring, Evaluation and Reporting
Strategy (http://www.environment.nsw.gov.au/soc/stateofthecatchmentsreport.htm, Muschal et al.
2010) and NSW State of the Environment reporting
(http://www.environment.nsw.gov.au/soe/soe2009/) and at local government area (Gilligan 2010b)
and catchment scales (Butler et al. 2012).
The assessment of fish assemblage condition reported upon for the Lower Murray-Darling CMA’s
monitoring program to date has only included individual assessment of the three SRA Nativeness
metrics and one of the three SRA Recruitment metrics. Calculation of the remaining metrics and
aggregating them into the three indicators and the overall index had not been possible prior to the
release of the technical papers describing their generation (Carter 2012; Robinson 2012). In this
report, the SRA analytical framework has been applied to the entire 2004 - 2012 time series of data
collected for the CMA’s fish monitoring program and represents a far more comprehensive
assessment of fish community health than had been possible previously.
Expectedness Indicator
The Expectedness Indicator (SR-FIe) represents the proportion of native species that are found
within a CMA management zone compared to the number historically present. SR-FIe is derived
from two input metrics; the observed native species richness divided by the RC-F corrected
expected species richness at each site (O/E), and the total native species richness observed within
the zone over the total number of species predicted to have existed within the CMA management
zone historically (O/P) (Robinson 2012).
SR-FIe had remained within the ‘Poor Condition’ band (40 < SR-FIe < 60) throughout the period
between 2004 and 2011, but dipped into the ‘Very Poor Condition’ band (20 < SR-FIe < 40) in
2012 (Figure 24) in response to the declining prevalence of several native species. There was a
statistically significant decline from SR-FIe = 55 ± 2 in 2011 to 34 ± 2 in 2012 (t
45
= 6.78,
p < 0.001) across the CMA area during the 2011/12 reporting period. Within individual CMA
management zones, SR-FIe declined from 71 ± 2 in 2011 to 24 ± 3 in 2012 (t
6
= 11.68, p < 0.001)
in the Darling River, 57 ± 4 in 2011 to 20 ± 1 in 2012 (t
7
= 10.07, p < 0.001) in Lakes, 57 ± 3 in
2011 to 29 ± 3 in 2012 (t
6
= 4.82, p = 0.003) in the upper Murray River and 36 ± 6 in 2011 to
22 ± 3 in 2012 (t
6
= 2.84, p = 0.030) in the Great Darling Anabranch.
Although there is no indication of an overall trend between 2004 and 2012 (Fisher’s Z = -0.431, p
= 0.666, Q
32
= 0.963, p = 0.963), the Expectedness of fish assemblages in 2012 is the lowest that it
has been since fish monitoring commenced in the CMA area (Figure 24).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 33
0
20
40
60
80
100
2004 2005 2006 2007 2008 2009 2010 2011 2012
Year
SR-FIe
Good
Moderate
Poor
Very Poor
Extremely Poor
Figure 24. Annual change in the average (± SE) Expectedness Indicator (SR-FIe) across the
Lower Murray-Darling CMA area between 2004 and 2012.
Recruitment Indicator
The Recruitment Indicator (SR-FIr) represents the recent reproductive activity of the native fish
community and is derived from three input metrics; the proportion of native species showing
evidence of recruitment at a minimum of one site within a zone, the average proportion of sites
within a zone at which each species captured was recruiting (RC-F corrected), and the average
proportion of total abundance of each species that are new recruits (Figure 25).
SR-FIr was within the ‘Moderate Condition’ band (60 < SR-FIr < 80) when the fish community of
the CMA area was initially benchmarked in 2004, but declined gradually into the Poor Condition
band as drought conditions persisted through until 2009 (Figure 26). Native fish recruitment
metrics in the Darling River, Lakes (principally the Menindee Lakes), Great Darling Anabranch
and Lower Murray River zones then increased in response to moderate flooding in the Darling
River (and reaches downstream) between January and April 2010 (Figures 1 & 26). However, SR-
FIr then dropped back into the Poor Condition band following the major flooding and subsequent
protracted hypoxic blackwater flows that occurred throughout the spring, summer and autumn
period prior to sampling in 2011 and declined even further into the Very Poor Condition band
following the major CMA-wide flooding that occurred in the Darling River from December 2011
and in the Murray River from March 2012. However, the annual change during the 2011/12 annual
reporting period was not statistically significant.
The overall trend between 2004 and 2012 has been a statistically significant and spatially
consistent decline in native fish recruitment (Fisher’s Z = -5.752, p <0.001, Q
32
= 15.799, p =
0.993), with recruitment of native fishes in 2012 being the lowest that it has been since fish
monitoring commenced in the CMA area (Figure 26).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
34 Fisheries Research Report Series: No. 32
Figure 25. Native fish recruitment metrics representing 1) the average proportion of sites at
which each native fish is recruiting (SRA Recruitment Metric 1), 2) the proportion
of native fish recruiting somewhere within each zone (SRA Recruitment Metric 2)
and 3) the average proportion of abundance of each native species that are new
recruits (SRA Recruitment Metric 4).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 35
0
20
40
60
80
100
2004 2005 2006 2007 2008 2009 2010 2011 2012
Year
SR-FIr
Good
Moderate
Poor
Very Poor
Extremely Poor
Figure 26. Annual change in the average (± SE) Recruitment Indicator (SR-FIr) across the
Lower Murray-Darling CMA area between 2004 and 2012.
Nativeness Indicator
The Nativeness Indicator (SR-FIn) represents the proportion of native versus alien fishes and is
derived from three input metrics: proportion native biomass (Figure 27), proportion native
abundance (Figure 28) and proportion native species (Figure 29) and is the most similar to the
CMAs existing CAP targets for native:alien ratios.
The proportion of total biomass that is native is the total weight of native fish collected divided by
the total weight of individuals (native plus alien species). During the 2011/12 reporting period, the
average proportion of total biomass that was native had increased significantly in the lower Murray
River (from 0.12 ± 0.06 in 2011 to 0.40 ± 0.09 in 2012, t
6
= -4.72, p = 0.003) and upper Murray
River (from 0.08 ± 0.08 in 2011 to 0.28 ± 0.05 in 2012, t
6
= -3.87, p = 0.008) zones. But there was
no significant change over the entire CMA area. In 2012, the average proportion of total biomass
that was native fish was lowest in the Lakes (0.08), followed by the Great Darling Anabranch
(0.12), floodplain wetlands (0.26), upper Murray River (0.28), Darling River (0.35) and was
greatest in the lower Murray River (0.40) (Figure 27). The only sites where biomass remained
dominated by native fish were Lelma and Pomona on the Darling River, Tangles Corner in the
upper Murray River zone, Ned’s Corner in the lower Murray River zone and the floodplain wetland
Peacock Creek. There was little spatial clustering of sites where native fish were dominant (Figure
27). The overall trend between 2004 and 2012 has been a statistically significant and spatially
consistent decline in the proportion of total biomass that is native fish (Fisher’s Z = -4.943, p
<0.001, Q
32
= 25.123, p = 0.801).
The proportion of total abundance that is native is the number of individual native fish collected
divided by the total number of individuals (native plus alien species). During the 2011/12 reporting
period, the average proportion of total abundance that was native had increased significantly in the
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
36 Fisheries Research Report Series: No. 32
Figure 27. Proportion of total fish biomass that is made up by native species in the Lower
Murray-Darling River system in 2012.
upper Murray River (from 0.19 ± 0.09 in 2011 to 0.69 ± 0.04 in 2012, t
6
= -8.86, p < 0.001) and
lower Murray River (from 0.38 ± 0.21 in 2011 to 0.79 ± 0.05 in 2012, t
6
= -4.94, p = 0.003). There
was a significant increase over the entire CMA area, increasing from 0.44 ± 0.05 in 2011 to 0.61 ±
0.04 in 2012 (t
45
= -2.85, p = 0.006). In 2012, the average proportion of total abundance that was
native fish was lowest in the Darling River (0.40), followed by the Great Darling Anabranch (0.56),
Lakes (0.59), floodplain wetlands (0.63), the upper Murray River (0.69) and was greatest in the
lower Murray River (0.79) (Figure 28). Whilst five of the seven Darling River sites remained
dominated by alien species, a majority of sites in other CMA management zones had returned to
the pre-2011 flood condition where total abundance was dominated by native species. The overall
trend between 2004 and 2012 has been a statistically significant and spatially consistent decline in
the proportion of total abundance that is native fish (Fisher’s Z = -6.681, p <0.001, Q
32
= 19.123, p
= 0.965).
The proportion of total species richness that are native species is the number of different native
species collected at a site divided by the total species richness (native plus alien species). During
the 2011/12 reporting period, the only CMA zone where the average proportion of total species
richness that was native had changed to a significant extent was the Lakes, where the proportion
had declined from an average of 0.72 ± 0.11in 2011 to 0.61 ± 0.04 in 2012 (t
7
= 4.56, p = 0.003).
But over the whole CMA area, there was no significant change in the proportion of total species
richness that was native. In 2012, the average proportion of total species richness that was native
fish was lowest in the Great Darling Anabranch (0.59), followed by the Lakes (0.61), floodplain
wetlands (0.64), lower Murray River zone (0.66), Darling River (0.67) and was greatest in the
upper Murray River zone (0.75) (Figure 29). Lake Wetherell was the only site sampled in 2012
where species richness was dominated by alien species, although there were an additional seven
sites where the
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 37
Figure 28. Proportion of total fish abundance that is made up of native species in the Lower
Murray-Darling River system in 2012.
number of native and alien species were equal (Figure 29). There were no sites where alien species
were absent. The overall trend between 2004 and 2012 has been a statistically significant decline in
the proportion of total species richness that is native fish (Fisher’s Z = -4.699, p < 0.001).
However, there was spatial variability in the trend (Q
32
= 51.219, p = 0.017) with statistically
significant declines in the upper (Fisher’s Z = -3.238, p = 0.001, Q
6
= 13.488, p = 0.036) and lower
(Fisher’s Z = -3.679, p < 0.001, Q
6
= 10.517, p = 0.105) Murray River zones and Lakes (Fisher’s Z
= -2.347, p = 0.019, Q
5
= 2.333, p = 0.801), but no significant trends in the Darling River (Fisher’s
Z = -0.054, p= 0.957, Q
6
= 2.397, p = 0.880) or floodplain wetlands (Fisher’s Z = -0.361, p = 0.718,
Q
4
= 6.329, p = 0.176). Significant heterogeneity within the upper Murray River zone was because
the declines were statistically significant at The Boiler (p < 0.001) and Wemen (p = 0.02), but not
at the remaining five sites within the zone.
The aggregated Nativeness indicator remained mostly in Moderate condition (60 < SR-FIn < 80)
from 2004 through until 2009 but dropped to Poor condition through 2010 – 2012 (particularly in
2011) (Figure 30) as a result of the increased biomass, abundance and prevalence of alien fishes in
response to higher flows. However, SR-FIn had started to recover in the Murray River zones,
increasing from 34 ± 2 in 2011 to 65 ± 3 in 2012 (t
6
= -7.20, p < 0.001) in the upper Murray River
CMA management zone and from 40 ± 4 in 2011 to 69 ± 6 in 2012 (t
6
= -3.77, p = 0.009) in the
lower Murray River zone during the 2011/12 reporting period. Despite SR-FIn declining from
58 ± 8 in 2011 to 46 ± 7 in 2012 (t
7
= 2.57, p = 0.037) in Lakes, the overall CMA-wide change
over the past year was an increase in average SR-FIn from 46 ± 3 in 2011 to 55 ± 3 in 2012 (t
45
= -
2.06, p = 0.044). The overall trend between 2004 and 2012 has been a significant decline in
Nativeness (Fisher’s Z = -6.676, p < 0.001, Q
32
= 24.498, p = 0.826), with the lowest point being
2011 (Figure 30).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
38 Fisheries Research Report Series: No. 32
Figure 29. Proportion of total fish species richness that are native species in the Lower
Murray-Darling River system in 2012.
Overall fish condition
After aggregating the Expectedness, Recruitment and Nativeness Indicators, the SRA Fish
Condition Index (SRA ndxFS) characterised fish assemblages as in Poor condition when
benchmarked across the CMA area in 2004 (Figure 31). Fish assemblages remained poor (or even
declined slightly) through until 2010, when Recruitment and to a lesser extent Expectedness
improved as a result of moderate flooding in the Darling River and downstream reaches in early
2010. However, decreases in recruitment and nativeness in 2011 (associated with widespread major
flooding and a subsequent protracted hypoxic blackwater event), and further decreases in
recruitment and expectedness in 2012 (associated with a second major widespread flood event),
have resulted in current fish assemblages being in Very Poor condition across the CMA area
(Figure 31).
During the 2011/12 reporting period declines in overall fish condition were statistically significant
in the Darling River (ndxFS = 55 ± 2 in 2011 to 14 ± 1 in 2012, t
6
= 13.00, p < 0.001) and Lakes
(61 ± 5 in 2011 to 13 ± 2 in 2012, t
7
= 11.20, p < 0.001) CMA management zones. A statistically
significant increase occurred in the Lower Murray River zone (27 ± 1 in 2011 to 33 ± 2 in 2012, t
6
= -2.82, p = 0.030). Across the entire CMA area, there was a significant decline in overall fish
condition over the past year (39 ± 3 in 2011 to 25 ± 2 in 2012, t
45
= 8.26, p < 0.001).
The overall trend between 2004 and 2012 has been a significant decline in overall fish condition
(Fisher’s Z = -5.023, p < 0.001, Q
32
= 17.344, p = 0.984), with the condition of fish assemblages in
2012 the lowest that it has been since fish monitoring commenced in the CMA area (Figure 31). As
at 2012, current fish condition is Extremely Poor in the Lakes (ndxFS = 13 ± 2) and Darling River
(14 ± 1) CMA management zones, Very Poor in the Great Darling Anabranch (22 ± 2), Upper
Murray River (23 ± 2) and lower Murray River (33 ± 2), and Poor in floodplain wetlands (41 ± 3)
(Figure 32).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 39
0
20
40
60
80
100
2004 2005 2006 2007 2008 2009 2010 2011 2012
Year
SR-FIn
Good
Moderate
Poor
Very Poor
Extremely Poor
Figure 30. Annual change in the average (± SE) Nativeness Indicator (SR-FIn) across the
Lower Murray-Darling CMA area between 2004 and 2012.
0
20
40
60
80
100
2004 2005 2006 2007 2008 2009 2010 2011 2012
Year
SRA ndxFS
Good
Moderate
Poor
Very Poor
Extremely Poor
Good
Moderate
Poor
Very Poor
Extremely Poor
Figure 31. Annual change in the average (± SE) Fish Condition Index (SRA ndxFS) across the
Lower Murray-Darling CMA area between 2004 and 2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
40 Fisheries Research Report Series: No. 32
Figure 32. Annual changes in the average (± SE) Fish Condition Index (SRA ndxFS),
Expectedness (SR-FIe), Recruitment (SR-FIr) and Nativeness (SR-FIn) Indicators
within each Lower Murray-Darling CMA management zone between 2004 and
2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 41
OTHER FISH ASSEMBLAGE PARAMETERS USEFUL FOR
UNDERSTANDING THE ‘HEALTH’ OF FISH
COMMUNITIES
Species richness
Species richness is the total number of different species occurring at a site, including native and
alien species. Average total species richness changes as the distribution of individual species within
the assemblage changes or as they become more or less prevalent across sites. In 2012, average
total species richness was lowest in the Great Darling Anabranch and Darling River (4.3 species
per site), followed by Lakes (4.6), floodplain wetlands (6.1), the upper Murray River zone (6.4)
and was greatest in the lower Murray River zone (8.0) (Figure 33). During the 2011/12 reporting
period, total species richness had declined from 8.7 ± 1.4 species per site in 2011 to 4.3 ± 0.5 in
2012 (t
6
= 5.27, p = 0.002) in the Darling River and from 10.6 ± 2.0 in 2011 to 6.4 ± 0.6 in 2012 (t
6
= 3.60, p = 0.011) in the upper Murray River (Figure 33).
Analysing data for native and alien species separately indicated that the decline in the Darling
River was driven by a decline in prevalence of both native (from 6.1 ± 0.4 in 2011 to 2.9 ± 0.3 in
2012, t
6
= 5.81, p = 0.001) and alien species (from 2.6 ± 0.2 in 2011 to 1.4 ± 0.2 in 2012, t
6
= 3.36,
p = 0.015) (Figure 34). In contrast, in the upper Murray River zone the decline in total species
richness was because of a decline in prevalence of alien species (from 3.6 ± 0.2 in 2011 to 1.6 ± 0.2
in 2012, t
45
= 5.29, p = 0.002) (Figure 34). Average native species richness also declined
significantly in the Lakes CMA management zone (from 4.1 ± 0.4 in 2011 to 2.8 ± 0.2 in 2012, t
7
=
3.27, p = 0.014) (Figure 34), but slight increases in alien species richness meant that there was no
net decline in total species richness.
Across the entire CMA area, total species richness declined from an average of 7.6 ± 0.5 species
per site in 2011 to 5.4 ± 0.3 in 2012 (t
6
= 4.39, p < 0.001), because of significant declines in the
prevalence both native (from 5.0 ± 0.3 in 2011 to 3.7 ± 0.3 in 2012, t
45
= 4.24, p < 0.001) and alien
(from 2.5 ± 0.2 in 2011 to 1.9 ± 0.1 in 2012, t
45
= 2.95, p = 0.005) species (Figures 33 & 34).
There is no statistically significant trend for total species richness between 2004 and 2012 (Fisher’s
Z = 1.200, p = 0.230, Q
32
= 26.412, p = 0.745). However, whilst the native species richness has not
changed (Fisher’s Z = -1.117, p = 0.264, Q
32
= 24.008, p = 0.844), the alien species richness has
increased (Fisher’s Z = 5.156, p < 0.001, Q
32
= 28.661, p = 0.636).
Total abundance
Total abundance is the total number of individuals sampled from a site, including native and alien
fish. In 2012, average total abundance was lowest in the lower Murray River zone (51 individuals
per site), followed by the upper Murray River zone (53), Great Darling Anabranch (58), Darling
River (123), Lakes (172) and was highest in floodplain wetlands (213) (Figure 35).
During the 2011/12 reporting period, total abundance had declined from 1,828 ± 578 individuals
per site in 2011 to 123 ± 80 in 2012 (t
6
= 14.37, p < 0.001) in the Darling River and from 376 ±
177 in 2011 to 53 ± 7 in 2012 (t
6
= 7.63, p < 0.001) in the upper Murray River (Figure 35).
Analysing data for native and alien species separately indicated that the decline in the Darling
River was driven by a decline in abundance of both native (from 694 ± 236 in 2011 to 34 ± 15 in
2012, t
6
= 9.01, p < 0.001) and alien species (from 1,134 ± 144 in 2011 to 90 ± 66 in 2012, t
6
=
7.99, p <0.001) (Figure 36).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
42 Fisheries Research Report Series: No. 32
Figure 33. Total species richness for fish in the Lower Murray-Darling River system in 2012.
Figure 34. Average (± SE) total species richness of native (above) and alien (below) fishes in each
CMA management zone and the overall Lower Murray-Darling CMA area
(excluding wetlands) between 2004 and 2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 43
Figure 35. Total abundance of fish in the Lower Murray-Darling River system in 2012.
Figure 36. Average (± SE) total abundance of native (above) and alien (below) fishes in each
CMA management zone and the overall Lower Murray-Darling CMA area
(excluding wetlands) between 2004 and 2012. Note the log scale on the Y axis.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
44 Fisheries Research Report Series: No. 32
This was also the case in the upper Murray River zone, where the decline in total abundance was
also because of a decline of both native (from 65 ± 11 in 2011 to 37 ± 7 in 2012, t
6
= 3.12, p =
0.021) and alien species (from 312 ± 64 in 2011 to 16 ± 3 in 2012, t
6
= 9.26, p < 0.001) (Figure
36). Alien abundance also declined significantly in the lower Murray zone (from 230 ± 50 in 2011
to 51 ± 12 in 2012, t
6
= 3.68, p = 0.010) (Figure 36). However, slight increases in native species
abundance meant that there was no net decline in total abundance.
Across the entire CMA area, total abundance declined from an average of 737 ± 159 individuals
per site in 2011 to 131 ± 23 in 2012 (t
45
= 4.37, p < 0.001), because of significant declines in both
native (from 349 ± 130 in 2011 to 85 ± 17 in 2012, t
45
= 2.32, p = 0.025) and alien species (from
388 ± 82 in 2011 to 48 ± 14 in 2012, t
45
= 5.06, p < 0.001) (Figures 35 & 36).
There is no statistically significant trend for total abundance between 2004 and 2012 (Fisher’s Z =
1.871, p = 0.061, Q
32
= 25.882, p = 0.769). However, whilst the abundance of native fishes has not
changed (Fisher’s Z = -0.518, p = 0.605, Q
32
= 27.762, p = 0.681), the abundance of alien fishes
has increased (Fisher’s Z = 6.862, p < 0.001, Q
32
= 14.923, p = 0.996).
Total biomass
Total biomass is the total weight of all individuals sampled at a site, including native and alien fish.
In 2012, average total biomass was lowest in the Great Darling Anabranch and upper Murray River
zone (14 kg per site), followed by the Darling River (15 kg), floodplain wetlands (17 kg), Lakes
(19 kg) and was highest in lower Murray River zone (24 kg) (Figure 37).
During the 2011/12 reporting period, total biomass had declined dramatically from 195 ± 94 kg per
site in 2011 to 15 ± 7 in 2012 (t
6
= 11.16, p < 0.001) in the Darling River, from 87 ± 34 in 2011 to
14 ± 4 in 2012 (t
6
= 6.77, p < 0.001) in the upper Murray River and from 66 ± 48 in 2011 to 24 ± 3
in 2012 (t
6
= 4.16, p = 0.005) in the lower Murray River (Figure 37).
Analysing data for native and alien species separately indicated that the decline in the Darling
River was driven by declines in biomass of both native (from 24 ± 7 in 2011 to 4 ± 2 kg in 2012, t
6
= 4.47, p = 0.004) and alien species (from 172 ± 32 in 2011 to 11 ± 7 in 2012, t
6
= 12.29, p <0.001)
(Figure 38). However, declines in total biomass in the upper Murray River (from 81 ± 13 in 2011
to 11 ± 3 in 2012, t
6
= 6.57, p < 0.001) and lower Murray River (from 56 ± 13 in 2011 to 14 ± 3 in
2012, t
6
=3.76, p = 0.009) zones were driven by declines in alien species biomass alone (Figure
38).
Across the entire CMA area, total biomass declined from an average of 76 ± 13 kg per site in 2011
to 17 ± 3 in 2012 (t
45
= 4.54, p < 0.001), because of significant declines in both native (from 9 ±
2 kg in 2011 to 4 ± 1 in 2012, t
45
= 2.73, p = 0.009) and alien species biomass (from 67 ± 12 in
2011 to 13 ± 3 in 2012, t
45
= 4.05, p < 0.001) (Figures 37 & 38).
There has been a statistically significant and spatially consistent increase in total biomass between
2004 and 2012 (Fisher’s Z = 4.181, p < 0.001, Q
32
= 24.950, p = 0.808). However, the total
biomass of native fishes has not changed (Fisher’s Z = -0.739, p = 0.460, Q
32
= 22.843, p = 0.883)
and the change in total biomass is because of an increase in the total biomass of alien fishes
(Fisher’s Z = 5.029, p < 0.001, Q
32
= 22.992, p = 0.879).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 45
Figure 37. Total biomass (kg) of fish in the Lower Murray-Darling River system in 2012.
Figure 38. Average (±SE) total biomass of native (above) and alien (below) fishes in the each
CMA management zone and the overall Lower Murray-Darling CMA area
(excluding wetlands) between 2004 and 2012. Note the log scale on the Y axis.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
46 Fisheries Research Report Series: No. 32
Proportion of total catch suffering from a health condition
The proportion of total catch suffering from a health condition (ie. symptoms of disease or
parasites) is the number of individuals of any species that were affected by any form of health
condition, divided by the total number of individuals inspected at each site (ie. all measured
individuals). Health conditions observed in 2012 include (in descending order of occurrence):
anchor worm (Lerneae spp) (5.4% of individuals), ulceration-lesions (1.81%), fin rot (0.69%),
fungus (0.48%), wounds (0.41%), emaciation (0.26%), skeletal deformities (0.22%), haemorrhage
(0.09%) and cloudy-eye (0.09%). The proportion of individuals affected by anchor worm was the
highest yet recorded, the proportion affected by lesions/ulceration (potentially a symptom of
Epizootic Ulcerative Syndrome (EUS)(see Gilligan 2012)) remained high and the proportion
affected by fungus had returned to around pre-2011 levels (Figure 39). The percentage of
individuals affected by other health conditions has remained relatively stable (Figure 39).
During the 2011/12 reporting period, the only CMA management zone where the average
proportion of individuals affected by a health condition changed significantly was the lower
Murray River zone, where the proportion of individuals affected had increased from 2.6% in 2011
to 12% in 2012 (t
6
= -4.94, p = 0.002). There was no significant change in any other CMA
management zone or across the CMA area overall. In 2012, the average proportion of individuals
suffering from a health condition was lowest in the Lakes zone (4.3% affected), followed by the
Great Darling Anabranch (5.5%), floodplain wetlands (8.8%), the Darling River (10.1%), the upper
Murray River (11.7%) and was greatest in the lower Murray River zone (12.0%) (Figure 40).
The overall trend between 2004 and 2012 has been a statistically significant increase in the
proportion of fish suffering from a health condition (Fisher’s Z = 7.487, p < 0.001, Q
32
= 28.630, p
= 0.638) with the proportion of fish affected in 2012 the highest that it has been since fish
monitoring commenced in the CMA area (Figure 40).
The species of fish most heavily affected by symptoms of disease and parasites were Murray cod
(56% of individuals), silver perch (50%), goldfish (44%), golden perch (37%), freshwater catfish
(25%), Murray-Darling rainbowfish (20%), spangled perch (14%), common carp (11%), unspecked
hardyhead (9%), bony herring (1%) and Australian smelt (0.04%). For most of these species, this
represents a substantial increase in the proportion of individuals affected during the 2011/12
reporting period (Figure 41).
0.0
1.0
2.0
3.0
4.0
5.0
6.0
Anc
h
or
w
orm
Wound
s
Ulcers
/
lesi
o
ns
Fung
u
s
Fin
d
am
a
ge
H
ae
m
orr
ha
ge
Defo
r
mity
E
m
aci
a
ted
Cys
t
P
o
p-e
y
e
C
lou
d
y-e
y
e
Drop
sy
Health condition
Percentage of individuals affected
2004
2006
2007
2008
2009
2010
2011
2012
Figure 39. The percentage of individuals affected by the range of symptoms of disease or parasites
recorded within the CMA area between 2004 and 2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 47
Figure 40. Proportion of total fish catch that is suffering from a health condition in the Lower
Murray-Darling River system.
0 102030405060
Golden perch
Goldfish
Murray cod
Common carp
Bony herring
Australian smelt
Spangled perch
Silver perch
Redfin perch
Freshwater catfish
Murray-Darling rainbowfish
Unspecked hardyhead
Eastern gambusia
Carp-gudgeons
Flat-headed gudgeon
Percentage of individuals suffering a health condition
2004
2006
2007
2008
2009
2010
2011
2012
Figure 41. The percentage of individuals of each species affected by symptoms of disease or
parasites recorded within the CMA area between 2004 and 2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
48 Fisheries Research Report Series: No. 32
PROGRESS TOWARD THE LOWER MURRAY-DARLING
CATCHMENT ACTION PLAN FISH ‘NATIVENESS’
TARGETS FOR RIVERINE HEALTH
The Lower Murray-Darling CMA’s CAP riverine health catchment targets related to the fish
community are:
A 55% improvement in the native to introduced fish species ratio.
A 25% improvement in the native to introduced fish abundance ratio.
A 25% improvement in the native to introduced fish biomass ratio.
To test progress towards these targets, data collected in 2004 (Gilligan 2005) were used as the
benchmark for each of the target ratios.
As explained in Gilligan (2005), ratios are problematic indices given that a zero value in the
denominator, as occurs when no alien fishes are collected at a site, results in an invalid value.
Further, the ratio can be very large if the number of natives exceeds the number of aliens, violating
the assumption of normality important for many standard statistical tests. Between 2004 and 2012,
there have been several instances of fish community samples that did not collect any alien species,
preventing the calculation of ratios at those sites. To enable an assessment of changes, median
rather than the mean values were used, with variance around the median estimated by bootstrap re-
sampling of the data-set with 1,000 iterations with replacement, and calculating the average
standard deviation of the bootstrap replicates. To enable inclusion of those samples where only
native fishes were collected, the raw value for the native fishes was used in place of the violated
ratios (ie. equivalent to a single alien fish being collected). At those sites where no fish at all were
collected it was assumed the ratio was 0. Paired t-tests were used to test for statistical significance
of the change.
Native:alien species ratio
The CAP target of a 55% improvement in the native:alien species ratio was not met in any
catchment zone in 2012 (Figure 42). During the 2011/12 reporting period there were statistically
significant declines in the number of native species collected per site in the Lakes (t
7
= 3.27, p =
0.014) and Darling River (t
6
= 5.81, p = 0.001) CMA management zones and significant decreases
in the number of alien species collected in the upper Murray River zone (t
6
= 5.29, p = 0.002) and
Darling River (t
6
= 3.36, p = 0.015) (Figure 34). These changes led to a significant decrease in the
native:alien species ratio in the Lakes CMA management zone (t
7
= 4.56, p = 0.001), but no
significant changes in any other CMA management zone or across the catchment overall.
The overall trend over the current CAP reporting period between 2004 and 2012 has been a
significant decline in the native:alien species ratio (Fisher’s Z = -4.751, p < 0.001). However the
trend has not been spatially uniform across CMA management zones (Q
32
= 53.788, p = 0.009),
with no trend in the Darling River (Fisher’s Z = -0.077, p = 0.939, Q
6
= 2.714, p = 0.844) or
floodplain wetlands (Fisher’s Z = -0.879, p = 0.379, Q
4
= 4.607, p = 0.330), a consistent and
significant decrease in the Lakes (Fisher’s Z = -2.500, p = 0.012, Q
5
= 2.903, p = 0.715) and
significant but inconsistent decreases in both the upper (Fisher’s Z = -3.083, p = 0.002, Q
6
=
14.546, p = 0.024) and lower (Fisher’s Z = -3.377, p = 0.001, Q
6
= 13.046, p = 0.042) Murray
River zones. In the upper Murray River declines in the native:alien species ratio were significant at
The Boiler (p < 0.001) and Wemen (p = 0.026), non -significant at Boston Bend, Nangiloc Carina
Bend and Tangles Corner and the ratio increased (non-significant) at Yungera Island. In the lower
Murray River zone declines were significant at Upper Kulnine (p = 0.050), 10km below Lock 7 (p
< 0.001) and Hancock Hill – Wompinni (p < 0.001) but non-significant at the remaining four sites.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 49
Across the entire CMA area, the proportion of sites occupied by each alien species has increased
from an average of 30% in 2004 to 39% in 2012 while the proportion of sites occupied by each
native species has declined from an average of 40% in 2004 to 29% in 2012.
Native:alien abundance ratio
The CAP target of a 25% improvement in the native:alien abundance ratio was not met in any
catchment zone in 2012 (Figure 43). There were statistically significant declines in the abundance
of native fishes collected per site in the Darling (t
6
= 9.01, p < 0.001) and upper Murray River (t
6
=
3.12, p = 0.021) CMA management zones and significant declines in the abundance of alien fishes
collected in the upper Murray River zone (t
6
= 9.26, p < 0.001), Darling River (t
6
= 7.98, p < 0.001)
and lower Murray River zone (t
6
= 3.68, p = 0.010) during the 2011/2012 reporting period (Figure
36). These changes led to significant improvements in the native:alien abundance ratios in both the
upper Murray River (t
6
= -7.82, p < 0.001) and lower Murray River (t
6
= -5.73, p = 0.001) CMA
management zones over the past year.
The overall trend during the current CAP reporting period between 2004 and 2012 has been a
statistically significant and spatially consistent decrease in the native:alien abundance ratio
(Fisher’s Z = -6.275, p <0.001, Q
32
= 24.282, p = 0.834).
Native:alien biomass ratio
The CAP target of a 25% improvement in the native:alien biomass ratio was met in the lower
Murray River CMA management zone in 2012 (Figure 44). However, the target improvement was
not met within any other CMA management zone. There were statistically significant declines in
the total biomass of native fishes collected per site in the Darling (t
6
= 4.47, p = 0.004) CMA
management zone and significant declines in the biomass of alien fishes collected in the Darling (t
6
= 12.29, p < 0.001), upper Murray River (t
6
= 6.57, p < 0.001) and lower Murray River (t
6
= 3.76, p
= 0.009) zones during the 2011/2012 reporting period (Figure 38). These changes led to a
significant improvement in the native:alien biomass ratio in the upper Murray River (t
6
= -3.23, p =
0.018) CMA management zone over the past year. Whilst the native: alien biomass ratio exceeded
the CAP target in the lower Murray River zone in 2012, the result did not register as a statistically
significant change given the high variability between sites with the zone in 2012 (the CAP target
was exceeded at three of the seven sites but progress was poor or extremely poor at the remaining
four; Figure 47).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
50 Fisheries Research Report Series: No. 32
0
1
2
3
4
5
6
7
8
9
10
Lakes Darling Great Darling
Anabranch
Murray I Murray II Wetlands Total
Native : Alien species ratio
Benchmark
2006
2007
2009
2010
2011
2012
Target
Figure 42. Comparison of the median (± SD) native:alien species ratio observed in 2006,
2007, 2009, 2010, 2011 and 2012 with the benchmark (2004) and target (55%
improvement) ratios.
0
20
40
60
80
100
120
140
160
Lakes Darling Great Darling
Anabranch
Murray I Murray II Wetlands Total
Native : Alien abundance ratio
Benchmark
2006
2007
2009
2010
2011
2012
Target
Figure 43. Comparison of the median (± SD) native:alien abundance ratio observed in 2006,
2007, 2009, 2010, 2011 and 2012 with the benchmark (2004) and target (25%
improvement) ratios.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 51
0
1
2
3
4
5
6
7
Lakes Darling Great Darling
Anabranch
Murray I Murray II Wetlands Total
Native : Alien biomass ratio
Benchmark
2006
2007
2009
2010
2011
2012
Target
Figure 44. Comparison of the median (± SD) native:alien biomass ratio observed in 2006,
2007, 2009, 2010, 2011 and 2012 with the benchmark (2004) and target (25%
improvement) ratios.
The overall trend during the current CAP reporting period between 2004 and 2012 has been a
statistically significant and spatially consistent decrease in the native:alien biomass ratio (Fisher’s Z
= -4.072, p <0.001, Q
32
= 25.491, p = 0.786).
Figures 45, 46 and 47 are provided to gauge progress towards meeting CAP targets at individual
sites as at the end of the 2011/12 reporting period. Progress is quantified as the change in the
proportion observed since 2004, divided by the change that would be required to meet the CAP
target. For example, a change in the proportion native biomass of + 0.13 (0.44 in 2004 to 0.57 in
2012) would equal a 59% achievement of the CAP biomass target, which is a change of 0.22 (e.g.,
0.13/0.22 = 59%). In each of the report cards, progress towards the targets at each site is presented
as one of five categories:
1. CAP target exceeded – The ratio of native:alien fish is greater than the CAP target value
(progress > +100% of CAP target).
2. Good – The ratio of native:alien fish has increased since 2004 but has not yet exceeded the
CAP target (progress +25 to +99% of CAP target).
3. Stable – The ratio of native:alien fish has not changed substantially since 2004 (progress -
25 to +25% of CAP target).
4. Poor – The ratio of native:alien fish has decreased since 2004 (-25 to -99% of CAP target).
5. Very Poor – The ratio of native:alien fish has changed by more than the change required to
meet the CAP target, but in the opposite direction, since 2004).
To present an overall assessment that encompasses the three CAP targets (Figure 48), a score was
assigned to each of the progress categories defined above for each ratio, where: CAP target
exceeded = 3 points, Good = 1 point, Stable = 0 points, Poor = -1 point and Very poor = -3 points.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
52 Fisheries Research Report Series: No. 32
These points were summed across the three ratios. Overall progress towards the CAP targets was
defined based on the summed scores according to the following bands:
Score = 9: All CAP targets exceeded
Score >5: Very good progress
Score > 1: Good progress
Score = 0: No progress
Score < -1: Progress poor
Score < -5: Progress very poor
Figure 49 presents a bar graph displaying the proportion of sites sampled that fall into each of the
progress categories defined above for each of the previous four reporting periods.
Fisheries Research Report Series: No.32 Page 53
Figure 45. Progress towards the CAP target of a 55% improvement in the ratio of native:alien species as at 2012.
Fisheries Research Report Series: No.32 Page 54
Figure 46. Progress towards the CAP target of a 25% improvement in the ratio of abundance of native:alien species as at 2012.
Fisheries Research Report Series: No.32 Page 55
Figure 47. Progress towards the CAP target of a 25% improvement in the ratio of biomass of native:alien species as at 2012.
Fisheries Research Report Series: No.32 Page 56
Figure 48. Overall progress towards the Lower Murray-Darling CMA CAP Riverine health targets for native:alien fish as at 2012.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 57
0%
20%
40%
60%
80%
100%
2006 2007 2008 2009 2010 2011 2012
Year
Percentage of sites
All CAP targets exceeded
Very good progress
Good progress
No progress
Progress poor
Progress very poor
Figure 49. The proportion of sites in each progress category in each year of sampling since the
Lower Murray-Darling CMA commenced monitoring progress towards CAP
targets (after benchmarking native:alien fish ratios across the CMA area in 2004).
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
58 Fisheries Research Report Series: No.32
THREATENED FISH RE-INTRODUCTIONS
On 6 May 2011, 4,500 southern pygmy perch and 700 olive perchlet bred in captivity at the
Narrandera Fisheries Centre were released at Thegoa Lagoon and 4,500 captive bred southern
pygmy perch were released at Meilman in Washpen Creek (see Gilligan 2012 for further details).
Fish sampling was undertaken at Washpen Creek and Thegoa Lagoon 20 and 47 days after release
in 2011 respectively. Two southern pygmy perch were recaptured at Washpen Creek, but neither
species was recaptured at Thegoa Lagoon.
In 2012, Thegoa Lagoon was re-sampled on 25 February (295 days post-release) and Washpen
Creek on 29 March (328 days post-release). Neither species was collected at either site. Further, no
other sightings have been reported by other researchers or by community members at these sites or
anywhere else within the CMA area.
It is still too soon to conclude that the re-introductions were a failure based on these results. Further
and potentially more intensive sampling is required to determine whether any stocked individuals
survived their first year at liberty or whether recruitment has occurred.
Table 7. Fish assemblages collected at the Washpen Creek and Thegoa Lagoon < 1 year after
the release of ~4,500 southern pygmy perch at Washpen Creek and ~4,500 southern
pygmy perch and 700 olive perchlet at Thegoa Lagoon on 6 May 2011. Threatened
species are shaded.
Site Species
Number of individuals
collected in 2011
Number of individuals
collected in 2012
Washpen Creek Bony herring 19 68
Carp-gudgeon species complex 40 145
Common carp 92 40
Eastern mosquitofish 46 2
Freshwater catfish 5 1
Golden perch 3 1
Goldfish 4 45
Murray-Darling rainbowfish 2 0
Silver perch 1 0
Southern pygmy perch 2 0
Unspecked hardyhead 25 15
Thegoa Lagoon Australian smelt 25 0
Bony herring 2 114
Carp-gudgeon species complex 8 1
Common carp 81 111
Eastern mosquitofish 1 2
Golden perch 2 8
Goldfish 43 54
Murray-Darling rainbowfish 3 0
Unspecked hardyhead 15 0
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 59
DISCUSSION
Data collected in the 2011/12 reporting period indicate that of the three Lower-Murray-Darling
Catchment Action Plan (CAP) Riverine Health targets to improve the native to introduced fish
ratios (55% improvement in native to alien species ratio, 25% improvement in abundance ratio and
25% improvement in biomass ratio), only the biomass ratio target was exceeded in the lower
Murray River CMA management zone in 2012 (Figure 44). Progress towards meeting the CAP
targets within each of the CMA river management zones is predominantly rated as poor to very
poor, with native:alien ratios getting worse at 71% of monitoring sites since 2004 (Figure 49).
Substantial changes in the distribution/prevalence, abundance and biomass of individual native and
introduced species have occurred as a result of major natural disturbance events during the CAP
period, including significant drought, major flood events and widespread and protracted hypoxic
blackwater flows. Together, these disturbances have generally resulted in significant deterioration
of all three CAP target ratios over the past eight years. As at 2012, the native:alien species ratio has
declined from a median of 4 ± 0.5 native species to every introduced species per site in 2004 to 2 ±
1 natives per introduced species in 2012, the native:alien abundance ratio has declined from a
median of 12 ± 3 native individuals to every introduced individual per site in 2004 to 2 ± 7 natives
per introduced individual in 2012 and the native:alien biomass ratio has declined from a median of
792 ± 187 grams of native fish to every 1 kilogram of introduced fish per site in 2004 to 187 ± 182
grams per kilogram of introduced fish in 2012.
A risk with relying on nativeness as the sole condition indicator (either ratios or proportions) is that
condition scores could fail to increase despite an increase in distribution/prevalence, abundance and
biomass of native species if the distribution/prevalence, abundance and biomass of introduced
fishes increases at the same or a faster rate. Whilst that in itself would indicate no improvement in
the fish assemblage condition, it is informative to understand the nature of the change (or lack
thereof). To address this uncertainty, changes in species richness, abundance and biomass of native
and introduced species groups were assessed and both were found to be declining for all three
parameters. Across the entire CMA area, average native species richness has declined by 29% and
alien species richness by 24%, native abundance has declined by 82% and alien abundance by
88%, and native biomass has declined by 56% while alien biomass has declined by 81% between
2011 and 2012.
Even more informative is an assessment of additional indicators of fish community health. For the
first time since the CMA monitoring program commenced, it has been possible to analyse the full
time series of data collected within the Lower Murray-Darling CMA area using the Sustainable
Rivers Audit procedure (Davies et al. 2010). In addition to generating an indicator of Nativeness,
the SRA process also generates indicators of species loss/recovery (Expectedness) and resilience
(Recruitment). And importantly, the SRA program developed a weighted expert rules system to
aggregate metrics and indicators into an overall fish community health index (Carter 2012). Over
the 2011/12 reporting period CMA-wide Expectedness had declined from a stable but poor
condition to very poor condition overall (Figure 24) in response to the declining prevalence of
several native species. However, although Expectedness of fish assemblages observed in 2012 is
the lowest that it has been since fish monitoring commenced in the CMA area, there is no
indication of an overall linear trend between 2004 and 2012. The Recruitment indicator was rated
as in Moderate condition when the fish community of the CMA area was initially benchmarked in
2004, but declined gradually to Poor condition as drought conditions persisted through until 2009
(Figure 26). Native fish recruitment in the Darling River, Lakes (principally the Menindee Lakes),
Great Darling Anabranch and Lower Murray River zones then rebounded to moderate condition in
response to moderate flooding in the Darling River (and reaches downstream) in early 2010 but
then dropped back into the poor condition band following the major flooding and subsequent
protracted hypoxic blackwater flows that occurred throughout the spring, summer and autumn
period prior to sampling in 2011 and declined even further into the very poor condition band
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
60 Fisheries Research Report Series: No.32
following the major CMA-wide flooding that commenced in the Darling River from December
2011 and in the Murray River from March 2012. Whilst the annual change during the 2011/12
reporting period was not statistically significant, there is a clear and significant overall trend of
declining native fish recruitment (and therefore native fish resilience) between 2004 and 2012, with
recruitment of native fishes in 2012 being the lowest that it has been since fish monitoring
commenced in the CMA area (Figure 26). As expected, the SRA’s Nativeness indicator mirrors the
CMA CAP ratios, deteriorating gradually from a moderate condition rating in 2004, to poor
condition in 2012 (Figure 30). Whilst, Nativeness did improve significantly to moderate condition
in the upper and lower Murray Rivers zones during the 2011/12 reporting period, the overall trend
between 2004 and 2012 has been a significant decline across the CMA area (as was suggested by
each of the individual native:alien ratios). Amalgamating the three indicators into a single Fish
Condition Index suggests that although the condition of the fish community has improved in the
lower Murray River CMA management zone (Figure 32), it has declined in the Darling River and
Lakes zones (Figure 32). Overall, the condition of the fish assemblages of the CMA area is very
poor and declining (Figure 31).
At the individual species level, three of the four species that have increased in prevalence since
2004 are alien species (native: spangled perch; aliens: eastern gambusia, redfin perch and goldfish)
and all six species that have decreased in prevalence are native fish (Murray-Darling rainbowfish,
flat-headed gudgeon, Murray cod, unspecked hardyhead, carp-gudgeons and Australian smelt).
Similarly, three of the seven species that have increased in abundance since 2004 are alien species
(aliens: common carp, goldfish and redfin perch; native: golden perch, spangled perch, silver perch
and bony herring) and all four species that have declined are natives (carp-gudgeons, unspecked
hardyhead, flat-headed gudgeon and Murray cod).
Notable positive changes in the abundance of individual species occurring during the 2011/12
reporting period were:
The collection of catfish in the lower Murray River zone for the first time in 2012.
Declines in the abundance of goldfish and eastern mosquitofish across most CMA zones.
A 84% decline in the abundance of carp following the 2011 recruitment boom (with carp
now only 3 times more abundant in 2012 than they were in 2004 – down from 21 times
more abundant in 2011)
No evidence that oriental weatherloach that invaded the CMA area in 2011 have
established populations.
Notable negative changes in the abundance of individual species occurring between 2011/12
reporting period were:
A decline in abundance of silver perch in the upper Murray River zone.
The virtual disappearance of the formerly common unspecked hardyhead from the
Murray River and its floodplain wetlands.
The anticipated decline or disappearance of spangled perch from many of the sites they
colonised during the 2010 and 2011 floods.
Little improvement in the abundance of Murray cod after declines observed following the
hypoxic blackwater flow event in the Murray River in 2011.
A 87% decline in the abundance of golden perch following the 2011 recruitment boom
(with golden perch now around the same abundance as in 2004)
Very large declines in the abundance of Murray-Darling rainbowfish across all CMA
zones
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 61
A 67% decline in the abundance of bony herring following the 2010 and 2011
recruitment boom (with bony herring now only 70% of their abundance in 2004).
The continued low abundance of Australian smelt in the upper Murray River zone and
decline in abundance in the Darling River.
The proportion of fish affected by a health condition continued to increase across most
CMA zones between 2011 and 2012.
Neither olive perchlet nor southern pygmy perch, the two threatened fishes reintroduced into
Thegoa Lagoon or Washpen Creek in May 2011 were recaptured at the release sites or any other
monitoring sites during sampling in 2012.
Together, these data suggest that the management actions implemented to June 2012 have not been
sufficient to result in much progress towards achieving the three Lower Murray-Darling CMA CAP
targets for fish community ‘nativeness’. The same recommended management actions suggested in
previous years still apply in 2012:
1. Implementing carp control programs. The abundance and biomass of carp must be
reduced in order to improve the native:alien abundance and biomass ratio riverine health
CAP targets. As suggested by Gilligan (2010, 2012), this could begin with funding or
otherwise facilitating or coordinating the use of the William’s Carp Separation Cages at
Locks 7, 8, 9, 10 and 15, and the installation of carp separation cages on fishways at
Burtundy Weir, Pooncarrie Weir and Weir 32. Subsidising the removal of carp by
commercial fisherman on a fee-for-service basis is also a viable option. However, both
removal strategies require a long-term commitment in order to maintain their
effectiveness. The Invasive Animals CRC is currently in the process of developing a long-
term biocontrol program for carp based on Cyprinid herpesvirus-3. But even if the virus is
approved for use in Australia, the earliest date at which the viral agent may be available
for release in the CMA area is 2016.
2. Threatened species recovery actions such as those described in the Fisheries NSW
Priorities Action Statement for threatened fish and marine vegetation. Murray hardyhead,
southern purple spotted gudgeon, olive perchlet, southern pygmy perch, flat-headed
galaxias and freshwater catfish would all benefit from fish-appropriate wetland
management, habitat rehabilitation and pest fish exclusion at key wetlands in the system.
Reintroduction programs for Murray hardyhead, southern purple spotted gudgeon and flat-
headed galaxias and continuation of the reintroduction programs for olive perchlet and
southern pygmy perch could lead to re-establishment of populations of each of these
locally extinct species in the CMA area. It is specifically recommended that the LMD
CMA continue to liaise with the Murray-Darling Freshwater Research Centre regarding
potential for reintroduction of the endemic southern basin form of the endangered southern
purple-spotted gudgeon (Hammer et al. 2009) and the critically endangered Murray
hardyhead to specific sites that meet their habitat requirements and can be managed by the
CMA to ensure ongoing survival of the reintroduced populations. The goal of these
threatened species recovery actions is to increase the ‘proportion of total species richness
that is native’ across the catchment, which is one of the Lower Murray-Darling riverine
health CAP targets.
3. Promoting the maintenance of large stable populations of large
adult Murray cod, golden
perch, silver perch and freshwater catfish in order to maximise the biomass of native fish
in fish communities and improve the ‘proportion of total biomass that is native’ (one of
the Lower Murray-Darling riverine health CAP targets). This could most readily be
achieved by promoting ‘catch and release’ of large individuals amongst the recreational
fishing community of the region. A current review of recreational fishing rules in NSW
(NSW Department of Primary Industries 2013) includes a proposal to reduce the bag and
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
62 Fisheries Research Report Series: No.32
possession limits for Murray cod and very importantly, the introduction of a catch and
release requirement for all Murray cod over 80 cm in length. If adopted, these changes are
likely to result in substantially increased biomass of Murray cod (and therefore native
fishes) throughout the CMA area. The data generated by the CMA’s monitoring program
represents one of the best data sets available to assess the flow on consequences of
improved Murray cod biomass on fish assemblages and overall ecosystem health.
2011/12 Lower Murray-Darling CMA CAP fish report, Gilligan
Fisheries Research Report Series: No. 32 63
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Other titles in the series
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Other titles in this series:
ISSN 1442-0147 (NSW Fisheries Research Report Series)
No. 1 Otway, N.M. and Parker, P.C., 1999. A review of the biology and ecology of the grey nurse shark
(Carcharias taurus) Rafinesque 1810. 36pp.
No. 2 Graham, K.J., 1999. Trawl fish length-weight relationships from data collected during FRV
Kapala surveys. 105pp.
No. 3 Steffe, A.S., Chapman, D.J. and Murphy, J.J., 1999. A description of the charter fishing boat
industry operating in the coastal and estuarine waters of New South Wales during 1997-98. 33pp.
No. 4 Reid, D.D. and Smith, I.R., 1998. The 1998 Pacific oyster survey. 14pp.
No. 5 Walford, T. and Pease, B., 2000. Strategies and techniques for sampling adult anguillid eels.
Proceedings of a workshop held at FRI, Cronulla, Australia, August 1999. 176pp.
No. 6 Heasman, M. and Lyall, I., 2000. Proceedings of the workshop held on 3 March 2000 at the
Sydney Fish Markets: Problems of producing and marketing the flat oyster Ostrea angasi in
NSW. 57pp.
No. 7 Heasman, M., 2003. Proceedings of the Sydney Rock Oyster Hatchery Workshop held on 8 and 9
August 2002 at Port Stephens, NSW. 164pp.
No. 8 Allan, G.A., 2003. Proceedings of the Aquafin CRC Snapper Workshop held on 26 September
2002 at the Convention Centre, Melbourne (Aquafin CRC 2001/208). 107pp.
No. 9 Faragher, R.A., 2004. Hooking mortality of trout: a summary of scientific services. 9pp.
No. 10 Daly, T., 2004. Summary of Proceedings from the Perkinsus Workshop held at the Cronulla
Fisheries Centre on 3 September 2003. 32pp.
ISSN 1449-9959
(NSW Department of Primary Industries - Fisheries Research Report Series)
No. 11 Baumgartner, L., 2005. Fish in Irrigation Supply Offtakes: A literature review. 22pp.
No. 12 Ganassin, C. and Gibbs, P., 2005. Descriptions of the wildlife species that commonly occur in the
marine and estuarine waters of NSW. 88pp.
No. 13 Nell, J., 2006. Manual for mass selection of Sydney rock oysters for fast growth and disease
resistance. 57pp + 110pp attachments.
No. 14 Gilligan, D. and Rayner, T., 2007. The distribution, spread, ecological impacts and potential
control of carp in the upper Murray River. 25pp.
No. 15 Baumgartner, L., 2007. Fish communities of the Nepean River in the vicinity of Pheasants Nest
Weir. 18pp.
No. 16 Gilligan, D., 2007. Annual progress report towards achievement of the Lower Murray Darling
Catchment Action Plan 2004 – 2015: Fish Community Monitoring 2005/06. 42pp.
No. 17 Gale, R., Silberschneider, V. and Stewart, J., 2007. A biological and economic assessment of the
2001 change in the Minimum Legal Length (MLL) of snapper in NSW. Report to the NSW Ocean
Trap & Line Management Advisory Committee, December 2007. 43 pp.
No. 18 Rowling, K., 2008. Review of ‘Bobbin Gear’ in the NSW Ocean Trawl Fishery. 15 pp.
No. 19 Baumgartner, L., Cameron, L., Faragher, B. and Pogonoski, J., 2008. An assessment of the trout
fishery in Oberon Dam and the Fish River. 23pp.
No. 20 O’Connor, W., Dove, M., Finn, B. and O’Connor, S., 2008. Manual for hatchery production of
Sydney rock oysters (Saccostrea glomerata). 53pp.
No. 21 Gillson, J.P., Scandol, J.P. and Suthers, I.M., 2008. Impacts of freshwater flow on catch rates of
estuarine fisheries resources in New South Wales. 66pp.
No. 22 Gilligan, D., 2008. Lower Murray-Darling Catchment Action Plan 2004 – 2016: Fish community
monitoring report card for 2006/07. 58pp.
Other titles in the series
68 Fisheries Research Report Series: No.32
ISSN 1837-2120 (Industry & Investment NSW – Fisheries Research Report Series)
No. 23 Ghosn, D., 2009. Data summary from the monitoring of Australian bass and native fisheries via
competition-based angling in NSW: 1988 – 2008. Interim Report. 74pp.
No. 24 Gilligan, D., 2009. Lower Murray-Darling Catchment Action Plan: Fish Community Monitoring
Report Card for 2008/09. 62pp.
No. 25 Knight, J.T. 2010. Penrith Lakes Fish Scheme – 2009 Fish Monitoring Program. 69pp.
No. 26 Stewart, J., Ballinger, G. and Ferrell, D., 2010. Review of the biology and fishery for Australian
sardines (Sardinops sagax) in New South Wales – 2010. 59pp.
No. 27 Stewart, J., Rowling, K., Hegarty, A-M. and Nuttall, A, 2010. Size and age at sexual maturity of
snapper Pagrus auratus in New South Wales 2008/09. 38pp
No. 28 Gilligan, D., 2010. Lower Murray-Darling Catchment Action Plan: Fish Community Monitoring
Report Card for 2009/10. 62 pp.
ISSN 1837-2120 (Fisheries Research Report Series)
No. 29 McKenzie, R.D. and Montgomery, S.S., 2012. A preliminary survey of pipis (Donax deltioides)
on the New South Wales south coast. 23pp.
No. 30 Ghosn, D., Collins, D., Baiada, C. and Steffe, A., 2012. Catch per unit effort and size composition
of striped marlin caught by recreational fisheries in southeast Australian waters. 34pp.
No. 31 Gilligan, D. 2012. Lower Murray-Darling Catchment Action Plan: Fish Community Monitoring
Report Card for the 2010/11 reporting period. 64pp.
No.32 Gilligan, D. 2012. Lower Murray-Darling Catchment Action Plan: Fish Community Monitoring
Report Card for the 2011/12 reporting period. 70pp.
Article
The spangled perch Leiopotherapon unicolor is considered a rare vagrant in the southern Murray-Darling Basin, Australia, due to its intolerance of the relatively cool water temperatures that prevail during winter months. This study details 1342 records of the species from 68 locations between 2010 and 2014 outside its accepted ‘core adult range’ following widespread flooding during 2010 and 2011. Although records of the species declined over 2013, L. unicolor remained resident in the southern Murray-Darling Basin as of April 2014. The species persisted in several locations for three consecutive winters with recruitment documented at two sites. This study represents the first identification of the dispersal of large numbers of L. unicolor into the southern Murray-Darling Basin, persistence beyond a single winter, and recruitment by the species in habitats south of its recognized ‘core adult range’. Targeted research would determine the potential for predicted environmental changes (artificially warmer drainage wetlands, climate change and greater floodplain connectivity) to facilitate longer term persistence and range expansion by the species in the southern Murray-Darling Basin.
Technical Report
Full-text available
The Southern Purple-spotted Gudgeon is a small, colourful freshwater fish with a distinct genetic conservation unit in the southern Murray–Darling Basin (MDB). The species underwent large declines in the region and was feared extinct, until it was recently (2002) rediscovered in the Lower Murray. The wild site has since dried (2007) owing to dramatic and rapid water level declines from the combined effects of heavy water use and prolonged drought across the MDB. Fortunately, fish were rescued from the site and these form the basis of a last resort captive breeding program. With the guidance of this document and support of stakeholders, a reintroduction program aims to reestablish the former wild site, create self-sustaining populations at other nearby sites, and develop backup refuge populations in isolated dams and wetlands. In the longer-term, sites upstream of Lock 1 would also be established to restore the former range. The general approach for reintroduction is moving away from mass release (‘hope for the best’) approaches, and towards investing in fewer but ‘trained’ fish that have a better chance of avoiding high initial mortality and that are released as part of broader restoration programs. Accordingly, the reintroduction plan is formed by review of a range of considerations regarding: the hatchery environment and procedures; release considerations tailored to the species; aspects of sites and restoration programs that lessen ultimate threatening processes; key knowledge gaps along the way; and factors such as permit requirements and stakeholder involvement. Recommendations for action and further investigation are made under relevant sub-headings. A specific output includes a stepwise flowchart that details likely criteria and actions between the identification of a potential release site and future establishment of a sustaining population. This is trialled to assess sites ready for immediate and future release in line with improving hatchery production and the finite life of captive broodstock.
Article
Flat-headed Gudgeon Philypnodon grandiceps were bred in ponds and aquaria at the Narrandera Fisheries Centre at temperatures from 18.0 to 28.0°C. Breeding in inland rivers probably occurs between October and April. An abundant food supply was essential for initiating spawning and the breeding display was recorded. Eggs were demersal, transparent, telolecithal and an elongated tear-drop shape with an adhesive disc at the pointed end. They measured 1.2 - 2.2 mm in length,by 0.7 - 0.9 mm in width, and were attached in clusters to solid objects. Oil globules were small and numerous at first, but coalesced to a single oil globule halfway to hatching. Eggs hatched in 4d 20h to 8d 8h after fertilisation at temperatures of 15.9 to 22.6°C. The total length of larvae at hatching was 3.15 to 4.32 mm and eyes were fully pigmented. The prolarval stage terminated at about 3d 12h after hatching, when length was 3.93 to 4.69 mm. The characteristic dark spot at the base of the caudal fin was present from the mid prolarval stage onwards. Males and females matured at one year old and were short lived. The largest fish collected was 11.0 cm TL. Up to 2020 ova were present in the ovaries and the Gono-somatic Index (G.S.I.) reached a maximum of 11.92 in females.