A survey of the fauna of the Roper River near Jude’s Photograph: P. Cowan Crossing in the late dry season 2013

Report number 02/2014D

www.nt.gov.au/lrm

This report can be cited as:

Dostine, P.L. (2014). A survey of the fish fauna of the Roper River near Jude’s Crossing in the late dry season 2013. Department of Land Resource Management. Report number 02/2014D. Palmerston, Northern Territory.

© Northern Territory of , 2014 ISBN 978-1-74350-053-8

Freshwater fish fauna of the Roper River ii

Executive summary

 Ground and surface water extraction during the dry season will reduce dry season flows in the Roper River and may impact ecological processes within the river. This report describes preliminary studies of the fish fauna of the Roper River, along a reach of the Roper River near Jude’s Crossing (14° 49’ S 134° 02’ E) on Flying Fox Station. The site is located in the middle reaches of the Roper River downstream of potential ground and surface water extractions for irrigation and mining use. The objective of the study was to assess appropriate sampling methods for quantitative description of fish communities within different stream habitats. Trials were conducted of the efficacy of bankside observation, gill-netting, and baited underwater video stations. The work is a precursor to the establishment of an environmental monitoring program linked to potential reductions in dry season flow.  The fish fauna of the middle reaches of the Roper River includes at least 35 from 21 families. The families (fork-tailed ), Plotosidae (eel-tail catfishes) and (grunters) are each represented by at least 4 species.  A field survey of the Roper River in the vicinity of Jude’s Crossing in late 2013 identified 23 species of fish. Twenty of these species were identified by direct observation, the remaining three (all ariid ) were collected by gill-netting in a main channel pool.  Eighteen species were recorded during standardised bankside observations of fish at 24 sites during day-time and night-time censuses. Species richness per site ranged from 4 to 12 species. Two species were ubiquitous (Melanotaenia splendida inornata) or nearly ubiquitous (Craterocephalus stercusmuscarum). Some species were more likely to be detected during day-time censuses (principally terapontid species); conversely some species were more likely to be detected during night-time censuses (principally small-bodied, sit-and-wait ambush predators). Results suggest that surveys based on direct observation can yield a high proportion of species present in the littoral zone, but that surveys need to include both day and night-time observations at individual sites.  Multi-panel gill-nets were used to capture seven fish species, including three species not recorded during bankside observations. Baited remote underwater video stations (BRUVS) were deployed in the same habitat as gill-nets and recorded at least five species of fish and two turtle species. Three of these fish species were not captured by gill-netting. Large numbers of fuliginosus were attracted to BRUVS; their numerical dominance will present difficulties quantifying relative abundance.  Further studies are needed to standardise sampling methods to derive a robust monitoring program for fish communities in the Roper River.

Freshwater fish fauna of the Roper River iii

Contents

1. Introduction ...... 2

2. Methods ...... 3 2.1 Fish fauna of the Roper River ...... 3 2.2 Bankside observations ...... 3 2.3 Multi-panel gill-nets ...... 4 2.4 Baited underwater video stations ...... 4 2.5 Environmental measurements ...... 5

3. Results ...... 8 3.1 Fish fauna of the Roper River ...... 8 3.2 Bankside observations ...... 8 3.2.1 Patterns of species richness ...... 12 3.2.2 Factors influencing probability of detection ...... 12 3.3 Multi-panel gill-nets ...... 14 3.4 Baited underwater video stations ...... 14 3.5 Environmental measurements ...... 16

4. Discussion ...... 17

5. Acknowledgements ...... 18

6. References ...... 18

7. Appendices ...... 19

Freshwater fish fauna of the Roper River 1 1. Introduction

The Roper River system is one of the largest river systems in northern Australia, with a catchment of over 80,000 km2 (Faulks 2001). Dry season flows within the main stem of the Roper are maintained by discharge from ground water aquifers in the upper reaches of the catchment. The extraction of water for mining operations and agriculture will diminish flow during the dry season, and potentially place stresses on the ecological processes of the river. Consequently there is a need to undertake research on the composition and dynamics of the biota of the river, and to develop monitoring approaches to guide and inform management. Previous studies of the fish fauna of the Roper system include Midgley (1979), Dally and Larson (2008), and Hammer et al. (2012). Dally and Larson (2008) recorded 18 species from a survey of a large waterhole on the Roper River bordering Elsey and Moroak stations in late September 2008. Hammer et al. (2012) recorded 27 species from a survey of 28 sites on a tributary of the Roper River on Wongalara Station, and listed an additional five species which are expected to occur, based on occurrence on adjoining properties. This report describes preliminary studies of the fish fauna of the Roper River, along a reach of the Roper River near Jude’s Crossing (14° 49’ S 134° 02’ E) on Flying Fox Station. The site is located downstream of potential mining operations which may require extraction of river water, and irrigated agriculture in the Mataranka area. The objective of the study was to assess appropriate sampling methods for quantitative description of fish communities within different stream habitats. Trials were conducted of the efficacy of bankside observation, gill- netting, and baited underwater video stations.

Freshwater fish fauna of the Roper River 2 2. Methods

Studies were conducted along a reach of the main channel Roper River near Jude’s Crossing (14° 49’ S 134° 02’ E) and a northern anabranch (14° 49’ S 134° 01’ E) on Flying Fox Station (Figure 1). Field trips were conducted in the late dry season of 2013. Flow in the Roper River at Jude’s Crossing was not measured; the anabranch ceased to flow late in the dry season after the field survey. However, flow in the main channel is likely to be equivalent to flow downstream at Red Rock (G9030250). Flow at Red Rock was estimated to be 2.51 m3/s on 25/10/13 (Wagenaar and Tickell 2013).

2.1 Fish fauna of the Roper River Records of fish species present in the middle section of the Roper River were compiled from previous surveys conducted by staff of NT Museum (Dally and Larson 2008) and Hammer et al. (2012), and from records of specimens of freshwater fish held by the NT Museum.

Figure 1. Satellite image of the eastern Top End of the Northern Territory showing boundary of Roper River catchment, Roper River drainage system, and location of study area.

2.2 Bankside observations Detection/non-detection data on fish species were collected by bankside observation within marked 15 m transects at 24 sites during two field trips from 28-29th August and 9-13th September 2013. Photographs of each site are shown in Figures 2 and 3; the locations of individual sites are given in Appendix 1. Censuses of ten minutes duration were conducted at each site on four occasions, two during daylight hours, mostly from 10:00 to 14:00; and two at night, mostly from 20:00 hours. Daytime observers were aided by Spotter polaroid sunglasses; night-time observations were aided by LED Lenser headlights. All fish species detected during each census were recorded. The identity of some specimens was confirmed

Freshwater fish fauna of the Roper River 3 by capture at the site during the survey using a hand net. There were ninety six individual site visits, though on two occasions the water surface at the site was covered with fallen leaves, and on these occasions no data were recorded. Sites were selected from the range of available river mesohabitats present in the study area including billabongs, backwaters, side channel and main channel. Data on water quality parameters were recorded at each site using a Quanta field meter (conductivity, temperature, dissolved oxygen and pH), and a Hach turbidity meter. Current speed was measured with an Ott propeller current meter 10 cm below the surface. The euphotic depth was calculated from a profile of photosynthetically available radiation with a LiCor sensor, and calculation of the attenuation coefficient. Deviations from expected values, if there were no biases in the probability of detection due to time of day, were calculated as the number of day-time records minus half the number of total records, for each species. The effect of time of day on the probability of detection of individual taxa was analysed using occupancy models as implemented in the software program PRESENCE v4.9 (Hines 2006). Several assumptions are associated with occupancy models and include the following: (1) species of interest occupy the site for the duration of sampling; (2) species are correctly identified; (3) the probability of detection of a species is independent of detecting the species at other sites; and (4) the probability of occupancy is constant across sites, or is a function of site covariates (MacKenzie and Kendall 2002; MacKenzie et al. 2002). These assumptions probably hold for most small- bodied littoral species which do not range widely or exhibit diurnal shifts in habitat. For each species two models were compared, the null model and a model containing the categorical covariate ‘time of day’ (day=1, night=0). The Akaike Information Criterion (AIC) was used as an objective means of model selection (Burnham and Anderson 2002), and the relative likelihood of candidate models was calculated using Akaike weights (wi) (Burnham and Anderson 2002). Model fit, based on 999 bootstrap simulations, was assessed within PRESENCE using the over-dispersion parameter ĉ. Lower and upper 95% confidence intervals of the probability of detection were estimated using the delta method (Ver Hoef 2012).

2.3 Multi-panel gill nets Two 35 x 2 m floating multi-panel gill nets were set on two occasions (27/8/13 and 11/9/13) an hour either side of dusk in a deep (>4 m) pool upstream of Jude’s Crossing. Surface-set nets with a drop of 2 m could not sample the entire water column, and benthic species were thus poorly sampled. Nets were monitored constantly for movement of surface floats indicating that fish had been netted. Most captured fish were extracted soon after capture and released immediately, some were retained as museum voucher specimens.

2.4 Baited underwater video stations Baited underwater video stations (BRUVS) were deployed at five sites in a pool upstream of Jude’s Crossing on 15th and 16th October 2103. BRUVS consisted of a square PVC frame weighted with dive weights at each corner, a vertical element holding a GoPro 3 high definition video camera in a waterproof housing, and a bait canister. Baits consisted of a mixture of pilchards and prawns on 15th October, and a mixture of peas and bread crumbs on

Freshwater fish fauna of the Roper River 4 16th October. BRUVS were deployed for approximately an hour at each site. At each site depth, turbidity, surface and bottom dissolved oxygen, current speed and euphotic depth were measured. Bottom substrate was noted from video recordings.

2.5 Environmental measurements Bankside survey sites were classified by mesohabitat and hydraulic environment. Hydrolab DataSonde loggers were deployed at three sites in main channel, backwater and billabong habitats to record diurnal patterns of dissolved oxygen concentrations in surface waters.

Freshwater fish fauna of the Roper River 5

R1 R2

R3 R4

R5 R6

R7 R8

R9 R10

R11 R12

Figure 2. Bankside observation survey sites 1-12, Jude’s Crossing, Roper River.

Freshwater fish fauna of the Roper River 6

R13 R14

R15 R16

R17 R18

R19 R20

R21 R22

R23 R24

Figure 3. Bankside observation survey sites 13-24, Jude’s Crossing, Roper River.

Freshwater fish fauna of the Roper River 7 3. Results

3.1 Fish fauna of the Roper River At least 35 fish species belonging to 21 families are known to occur in the middle and upper reaches of the Roper River and its tributaries (Table 1). There is some uncertainty within some groups, and further collecting and taxonomic work will clarify the status of several species, or reveal additional species, particularly within the families , Ariidae and Gobiidae. The ambassid listed as sp. probably corresponds to the species listed as Ambassis sp. (agrammus/muelleri) northwest glassfish in Hammer et al. (2012), and which has characters which are intermediate between those of A. agrammus and A. muelleri. Similarly, the freshwater sole Brachirus sp. of the Roper River possesses characters which are intermediate between those of B. selheimi and B. salinarum, and may represent a separate species. The composition of the ariid catfish fauna of the Roper River needs clarification, especially the status of taxa identified as berneyi and N. graeffei. The status of gobiid species also needs clarification. It is unclear whether flathead goby Glossogobius giurus occur in the Roper River. There is a record of black-striped rainbowfish Melanotaenia nigrans from the pump station pool on Flying Fox Station (D. Wilson pers. comm.). Photographs of selected species are shown in Figure 4.

3.2 Bankside observations Bankside censuses yielded 346 records of 18 fish taxa from 13 families (Table 2, Appendix 2), including most of the species expected to occur in littoral habitats in this section of the Roper River. Two additional species, Scleropages jardinii (Osteoglossidae) and Arramphus sclerolepis (Hemiramphidae), were recorded as incidental observations. Not all taxa could be identified to the level of species from bankside observation. The data may include multiple species for the genera Oxyeleotris (Eleotridae) and Glossogobius (Gobiidae). Two species of Oxyeleotris have been recorded from the Roper system (O. lineolata and O. selheimi), and there are at least two species in the Glossogobius. Families known to occur in the Roper but which were not recorded include Synbranchidae (swamp eel), Engraulidae (freshwater ), Megalopidae (oxeye herring), Pristidae (sawfish), Carcharhinidae (bull ) and Ariidae (fork-tailed catfish). At least three species of ariid catfish commonly occur within the study area, the remainder are likely to be rare on a regional scale. The tally of species recorded by visual observation alone compares favourably with other local surveys employing a variety of capture methods (e.g. Dally and Larson 2008), with the exception of ariid catfish.

Freshwater fish fauna of the Roper River 8

(a) (b)

(c) (d)

(e) (f)

Figure 4. Fish of the Roper River (a) highfin catfish , (b) shovelnose catfish N. paucus, (c) small-mouthed catfish Cinetodus froggatti, (d) freshwater sole Brachirus sp., (e) barred grunter percoides, (f) gulf grunter ogilbyi.

Freshwater fish fauna of the Roper River 9

Family Species name Common name Ambassidae Ambassis macleayi Macleay’s glassfish Ambassidae Ambassis sp. northwest glassfish mouth almighty Ariidae Cinetodus froggatti small-mouthed catfish Ariidae Neoarius berneyi highfin catfish Ariidae blue catfish Ariidae Neoarius paucus shovelnose catfish Ariidae Sciades leptaspis Atherinidae Craterocephalus stercusmuscarum fly-specked hardyhead Belonidae Strongylura krefftii freshwater longtom Carcharhinidae Carcharhinus leucas bull shark Centropomidae Lates calcarifer Clupeidae Nematalosa erebi bony bream Eleotridae Mogurnda mogurnda purple-spotted gudgeon Eleotridae Oxyeleotris lineolata sleepy cod Eleotridae Oxyeleotris selheimi giant gudgeon Engraulidae scratchleyi freshwater anchovy Gobiidae Glossogobius aureus golden flathead goby Gobiidae Glossogobius munroi square blotch goby Hemirhamphidae Arrhamphus sclerolepis snub-nosed garfish Megalopidae Megalops cyprinoides oxeye herring Melanotaeniidae Melanotaenia splendida inornata chequered rainbowfish Osteoglossidae Scleropages jardinii gulf saratoga Plotosidae Anodontiglanis dahli toothless catfish Plotosidae Neosilurus ater black catfish Plotosidae Neosilurus hyrtlii Hyrtl’s tandan Plotosidae Porochilus rendahli Rendahl’s catfish Pristidae Pristis microdon sawfish Soleidae Brachirus sp. freshwater sole Synbranchidae Ophisternon gutturale swamp eel Terapontidae Amniataba percoides barred grunter Terapontidae Hephaestus fuliginosus sooty grunter Terapontidae unicolor spangled perch Terapontidae Scortum ogilbyi gulf grunter Toxotidae Toxotes chatareus Sevenspot archerfish

Table 1. List of fish species known from middle reaches of the Roper River.

Freshwater fish fauna of the Roper River 10 Family name Species name Common name day night total freq Ambassidae Ambassis sp. northwest glassfish 1 1 2 2 Ambassidae Ambassis macleayi Macleay’s glassfish 16 22 38 14 Apogonidae Glossamia aprion mouth almighty 13 19 32 15 Atherinidae Craterocephalus stercusmuscarum fly-specked hardyhead 28 16 44 21 Belonidae Strongylura krefftii freshwater longtom 0 1 1 1 Centropomidae Lates calcarifer barramundi 0 9 9 7 Clupeidae Nematolosa erebi bony bream 6 1 7 4 Eleotridae Oxyeleotris sp. sleepy cod 1 9 10 8 Gobiidae Glossogobius sp. goby 1 8 9 9 Melanotaeniidae Melanotaenia splendida inornata chequered rainbowfish 43 38 81 24 Plotosidae Anodontiglanis dahli toothless catfish 0 1 1 1 Plotosidae Neosilurus ater black catfish 1 2 3 2 Soleidae Brachirus sp. freshwater sole 0 1 1 1 Terapontidae Amniataba percoides barred grunter 29 5 34 19 Terapontidae Hephaestus fuliginosus sooty grunter 14 1 15 10 Terapontidae spangled grunter 29 6 35 17 Terapontidae Scortum ogilbyi gulf grunter 2 0 2 2 Toxotidae Toxotes chatareus sevenspot archerfish 13 9 22 11 Total 197 149 346 24

Table 2. Number of records of fish species during day-time and night-time censuses, total number of records, and frequency of occurrence of fish species at 24 census sites.

Freshwater fish fauna of the Roper River 11 3.2.1 Patterns of species richness Taxa richness per site was similar for day-time (range 2 to 8, mean 5.2) and night-time censuses (range 2 to 10, mean 4.3) (Figure 5). Taxa richness per site for combined day and night-time censuses ranged from 4 to 12 taxa, with mean taxa richness per site of 7.0.

(a) (b)

(c)

Figure 5. Frequency histogram of species richness by site for (a) all data, (b) data from day-time censuses, and (c) data from night-time censuses.

3.2.2 Factors influencing probability of detection Censuses conducted during day-time yielded 197 records of 14 species, whereas censuses conducted at night yielded 149 records of 17 species (Table 2). The only species not recorded during night-time censuses was Scortum ogilbyi; four species only recorded at night include Strongylura krefftii, Lates calcarifer, Anodontiglanis dahli and Brachirus sp. Some species were primarily recorded in day-time censuses (principally terapontid species); whereas other species were primarily recorded in night-time censuses (Figure 6). Species primarily observed during night-time censuses include the sit-and-wait ambush predators Glossamia aprion, Glossogobius and Oxyeleotris. A bias in the probability of detection is borne out by the results of occupancy modelling. Data were sufficient for the modelling of ten species; models for six species had coefficients for the covariate time of survey with 95% confidence intervals that did not overlap with zero, indicating a significant effect of time of survey on the probability of detection of these species (Table 3). Of these, the coefficient was positive for five species, and negative for one species. For three terapontid species in particular, there was strong evidence that the probability of detection varies between day-time and night-time censuses (Table 4). For example, the probability of detection of sooty grunter Hephaestus fuliginosus was 0.59 during the day, but only 0.04 during night-time censuses. H. fuliginosus was observed to refuge beneath stream rocks at night. Similarly, the probability of detection of spangled grunter

Freshwater fish fauna of the Roper River 12 Leiopotherapon unicolor was 0.83 during the day, but only 0.17 during night-time censuses. Conversely, the probability of detection of sleepy cod Oxyeleotris sp. was 0.04 during day- time censuses, and 0.32 during night-time censuses.

Figure 6. Deviation from expected values of number of records for each species identified during bankside observations of freshwater fish in the Roper River.

Species ĉ wi Intercept Time of day Ambassis macleayi 1.03 0.65 1.45 (0.50) -1.09 (0.63) Amniataba percoides 1.30 1.00 -1.92 (0.48) 2.98 (0.63) Craterocephalus 0.95 stercusmuscarum 0.91 -0.53 (0.33) 1.14 (0.45)

Hephaestus fuliginosus 0.81 1.00 -3.13 (1.04) 3.48 (1.13) Leiopotherapon unicolor 1.06 1.00 -1.57 (0.45) 3.17 (0.66) Nematalosa erebi 0.61 0.90 -2.04 (1.08) 2.85 (1.34) Oxyeleotris sp. 0.75 0.96 -0.77 (0.81) -2.54 (1.11)

Table 3. Over-dispersion parameter (ĉ), Akaike weights, intercept and estimated coefficient (and one standard error) of covariate influencing the probability of detection of fish using visual assessment in the Roper River. Bold values represent coefficients that had 95% confidence intervals that did not overlap with zero.

Freshwater fish fauna of the Roper River 13

Probability of detection Species Day Night

Ambassis macleayi 0.59 (0.40-0.76) 0.81 (0.61-0.92) Amniataba percoides 0.74 (0.55-0.87) 0.13 (0.05-0.28) Craterocephalus stercusmuscarum 0.65 (0.48-0.79) 0.37 (0.24-0.53) Hephaestus fuliginosus 0.59 (0.30-0.83) 0.04 (0.01-0.25) Leiopotherapon unicolor 0.83 (0.64-0.93) 0.17 (0.08-0.33) Nematalosa erebi 0.69 (0.27-0.93) 0.12 (0.02-0.52) Oxyeleotris sp. 0.04 (0.00-0.25) 0.32 (0.09-0.69)

Table 4. Probability of detection for eight fish species during day-time and night-time censuses, with 95% confidence intervals.

3.3 Multi-panel gill-nets Multi-panel gill-nets captured at least seven fish species, including three ariid catfish species which were not detected by bankside observations (Table 5). Further studies are required to confirm the taxonomic identities of the three or more species of Neoarius in the Roper River. No non-target species were captured in gill-nets during this survey.

Species Family 27 Aug 13 11 Sep 13 Total % total Cinetodus froggatti Ariidae 2 2 4.3 Neoarius unid. Ariidae 6 6 13.0 Neoarius berneyi Ariidae 2 2 4.3 Neoarius paucus Ariidae 1 7 8 17.4 Lates calcarifer Centropomidae 1 1 2.2 Nematolosa erebi Clupeidae 14 4 18 39.1 Oxyeleotris lineolatus Eleotridae 1 1 2.2 Toxotes chatareus Toxotidae 7 1 8 17.4 Total 30 16 46

Table 5. Number of individual fish captured using multi-panel gill-nets on two occasions. Unidentified specimens of Neoarius sp. were probably either N. graeffei or N. berneyi.

3.4 Baited underwater video stations Baited underwater video stations were deployed at five sites within the pool upstream of Jude’s Crossing at depths ranging from 2.2 to 4.6 metres. Turbidity at these sites ranged from 1.2 to 1.8 NTU, and euphotic depth ranged from 5.5 to 7.6 metres (Table 6). These conditions allowed for the capture of video imagery of sufficient quality to identify most species, with the exception of ariid catfish. At least five fish species and two turtle species were observed on video imagery from 15th October (Table 7). Large numbers of Sooty grunters (Hephaestus fuliginosus) were attracted to baited stations; their numerical dominance will present difficulties quantifying relative

Freshwater fish fauna of the Roper River 14 abundance using standard measures for BRUVS such as the maximum number of individuals of each species present in a frame (Figure 7). There were no obvious differences in the response of fish to different bait types, though was no attempt to quantify the effect of bait type.

BR1 BR2 BR3 BR4 BR5

Start time 10:05 10:25 10:55 11:00 11:20 Depth (m) 2.2 3.6 4.6 3.7 2.3 Turbidity (NTU) 1.4 1.4 1.3 1.2 1.8

DO surface (mg/L) 5.55 5.84 5.58 5.66 5.76

DO bottom (mg/L) 5.62 5.82 5.62 5.66 5.71 Current speed (m/s) 0.09 0.08 0.07 0.14 0.16 Euphotic depth (m) 6.7 7.5 7.5 7.6 5.5 Bottom substrate rock/sand rock sand sand Chara

Table 6. Environmental parameters associated with five video deployment sites.

Species BR1 BR2 BR3 BR4 BR5 Fish Ambassis macleayi + + + + + Amniataba percoides + + + + + Hephaestus fuliginosus + + + + + Neoarius sp. + + + + + Toxotes chatareus + Turtles Elseya dentata + + + + Emydura subglobosa worrelli + + +

Table 7. Fish and turtle species detected by underwater video at five sites in a main channel pool upstream of Jude’s Crossing, Roper River.

Freshwater fish fauna of the Roper River 15 (a) (b)

Figure 7. Screen shots from underwater video at site BR5 in the Roper River (a) sooty grunter H. fuliginosus, and northern snapping turtle Elseya dentata; (b) sooty grunter H. fuliginosus, ariid catfish Neoarius sp. and barred grunter Amniataba percoides.

3.5 Environmental measurements There were marked fluctuations in dissolved oxygen concentration in backwater and billabong habitats, but relatively muted diurnal variation in main channel habitats (Figure 8). The diurnal range of dissolved oxygen was > 7 in shallow billabong waters, but <1 in the main channel (Table 8). Water quality data for each sites in presented in Appendix 3.

Figure 8. Diurnal patterns of dissolved oxygen at three sites in the Roper River, main channel, backwater and billabong.

Freshwater fish fauna of the Roper River 16

Date Mesohabitat DOmin (mg/L) DOmax (mg/L) DOrange min max 9 September 2013 Backwater 1.62 7.93 6.31 11 September 2013 Billabong 4.02 11.38 7.36 24 October 2013 Main channel 6.52 7.33 0.81

Table 8. Minimum, maximum and range of dissolved oxygen values recorded over diurnal cycles at 3 sites in Roper River.

Water quality parameters and habitat measurements at bankside observation sites are given in Appendix 3, 4 and 5.

4. Discussion

The results of this study indicate that direct observational methods can detect a significant portion of the littoral fish community in low turbidity streams and rivers of northern Australia. Advantages include the lack of need for nets and other equipment, and the ability to survey a large number of sites within a relatively short period. Disadvantages include a dependence on good viewing conditions, restriction to species typical of shallow littoral habitats, and safety issues associated with the potential presence of saltwater crocodiles. The study found that the time of survey, either day or night, influences the probability of detection of several species. Accordingly, survey and monitoring studies may need to incorporate both day and night censuses in survey design. Gill-netting yielded only seven species, though three of these species were not detected by bankside observation. The floating gill-nets did not sample the entire water column, and were unable to sample benthic fish communities. Assessment of the efficacy of gill-netting will require both surface-set and bottom-set nets. Gill-netting has several disadvantages including increased risk of injury or mortality of fish, and of non-target organisms such as turtles and crocodiles. No non-target species were captured during this survey. All fish captured were either released unharmed, or retained as voucher specimens. BRUVS were used to detect five species and two turtle species. This method holds some promise as a method for monitoring fish communities, provided that water clarity is high. The two principal impediments with BRUVS are difficulties with identification of some species, especially ariid catfish, and problems for quantification posed by the numerical dominance of sooty grunters. A list of fish specimens registered with the Northern Territory Museum is given in Appendix 6.

Freshwater fish fauna of the Roper River 17 5. Acknowledgements

The manager of Flying Fox Station Mark Sullivan generously provided access to Roper River study sites. Matt Majid and Simon Townsend provided valuable field assistance. Dave Wilson conducted most of the fish observation study, and provided assistance with gill-netting and other sampling activities. Simon Townsend provided comments on this report. Research was conducted under permit number 2013-2014/S17/3309 from the Northern Territory Department of Primary Industry and Fisheries, and licence number 011 from the Ethics Committee of Charles Darwin University.

6. References

Burnham, K.P. and Anderson, D.R. (2002). ‘Model Selection and Multimodel Inference: a Practical Information-theoretic Approach.’ (Springer-Verlag: New York.) Dally, G. and Larson, H.K. (2008). Roper River (Elsey and Moroak Stations) freshwater survey. MAGNT Research Report No. 12, November 2008. Faulks, J.J. (2001). An assessment of the physical and ecological condition of the Roper River and its major tributaries. Technical Report No. 36/2001, Natural Resources Division, Department of Lands, Planning and Environment, Katherine, NT. Hines, J.E. (2006). PRESENCE4 – Software to estimate patch occupancy and related parameters USGS-PWRC. MacKenzie, D.I. and Kendall, W.L. (2002). How should detection probability be incorporated into estimates of relative abundance? Ecology 83, 2387-2393. MacKenzie, D.I., Nichols, J.D., Lachman, G.B., Droege, S.J., Royale, A.J. and Langtimm, C.A. (2002). Estimating site occupancy rates when detection probabilities are less than one. Ecology 83, 2248-2255. Midgley, S.H. (1979). The Roper River system, Limmen Bight River system, Rosie Creek system in the Northern Territory. A biological resource study. Technical report, Fisheries Division, Northern Territory Department of Primary Production, pp. 1-43. Ver Hoef, J.M. (2012). Who invented the delta method? The American Statistician 66, 124- 127. Wagenaar, D. and Tickell, S.J. (2013). Late dry season stream flows and groundwater levels, upper Roper River, October 2013. Department of Land Resource Management. Report number 10/2013D. Palmerston, Northern Territory.

Freshwater fish fauna of the Roper River 18

8. Appendices

Appendix 1. Geographic coordinates of 24 fish survey sites.

Site Latitude Longitude Datum R1 -14.82156 134.03349 GDA94 R2 -14.82091 134.03323 GDA94 R3 -14.81987 134.03320 GDA94 R4 -14.81926 134.03323 GDA94 R5 -14.81923 134.03305 GDA94 R6 -14.81894 134.03294 GDA94 R7 -14.81816 134.03249 GDA94 R8 -14.81706 134.03252 GDA94 R9 -14.81563 134.03235 GDA94 R10 -14.81040 134.02252 GDA94 R11 -14.81010 134.02225 GDA94 R12 -14.80976 134.02231 GDA94 R13 -14.80959 134.02203 GDA94 R14 -14.80898 134.02228 GDA94 R15 -14.80902 134.02235 GDA94 R16 -14.80853 134.02248 GDA94 R17 -14.80763 134.02351 GDA94 R18 -14.80662 134.02396 GDA94 R19 -14.80616 134.02386 GDA94 R20 -14.80712 134.02350 GDA94 R21 -14.81950 134.03284 GDA94 R22 -14.81638 134.03180 GDA94 R23 -14.81895 134.03261 GDA94 R24 -14.80796 134.02325 GDA94

Freshwater fish fauna of the Roper River 19

Appendix 2. Detection/non-detection data for fish at 24 sites in the Roper River, summarised across four 10 minute surveys.

Species R1 R2 R3 R4 R5 R6 R7 R8 R9 R10 R11 R12 R13 R14 R15 R16 R17 R18 R19 R20 R21 R22 R23 R24 Ambassis sp. 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 Ambassis macleayi 0 1 1 1 0 0 0 1 0 1 1 0 1 0 1 0 1 1 1 1 0 1 0 1 Amniataba percoides 0 0 1 1 1 1 1 1 1 1 1 0 1 1 0 0 1 1 1 1 1 1 1 1 Anodontiglanis dahli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 Brachirus sp. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 Craterocephalus stercusmuscarum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 Glossamia aprion 1 1 1 1 1 0 0 1 0 1 0 0 0 1 1 0 1 1 1 1 0 1 0 1 Glossogobius sp. 0 0 0 0 1 1 0 0 1 0 0 1 1 0 0 1 0 0 0 0 0 1 1 1 Hephaestus fuliginosus 0 0 0 0 1 0 1 1 0 0 1 0 0 0 0 0 0 1 1 0 1 1 1 1 Lates calcarifer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 Leiopotherapon unicolor 1 0 0 1 1 1 0 1 1 1 1 1 1 1 0 1 1 0 0 0 1 1 1 1 Melanotaenia splendida inornata 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Nematalosa erebi 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 Neosilurus ater 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 Oxyeleotris sp. 0 0 0 0 1 0 0 0 0 1 1 0 1 1 0 1 1 1 0 0 0 0 0 0 Scortum ogilbyi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 Strongylura krefftii 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 Toxotes chatareus 0 1 1 1 0 1 0 1 0 0 1 0 0 0 0 0 1 0 1 1 1 1 0 0

Freshwater fish fauna of the Roper River 1 Appendix 3. Data for water quality parameters measured at 10 cm depth at 24 sites.

EC DO %sat Site Date Time Temp °C (uS/cm) (mg/L) pH DO Turbidity R1 28/8/13 20:38 24.5 1445 10.4 8.36 126.9 1.7 R2 28/8/13 20:45 23.6 1454 7.5 8.24 90 1.9a R3 27/7/13 10:00 23.7 1432 7.9 8.25 93.4 1.8b R4 28/9/13 21:10 23.6 1394 12.7 8.48 151.9 2.3 R5 28/9/13 21:20 23.6 1459 7.7 8.27 92.3 1.8b R6 28/9/13 21:30 23.5 1454 7.9 8.27 94 2.3 R7 28/8/13 21:40 23.5 1456 7.8 8.3 92.5 2.0b R8 28/8/13 21:50 23.3 1432 7.0 8.24 83.1

R9 28/8/13 22:10 23.4 1432 7.4 8.25 88.3 2.0 R10 11/9/13 11:20 24.5 2270 5.4 8.5 66.7 1.4 R11 11/9/13 11:10 24.3 1454 8.1 8.3 77.7 2.1 R12 11/9/13 11:00 24.6 1470 7.5 8.34 92.2 1.2 R13 11/9/13 10:45 24.8 1453 8.3 8.36 100.8 0.6 R14 11/9/13 10:35 24.2 1458 7.5 8.31 89.8 0.7 R15 11/9/13 10:25 25.1 1780 6.2 7.97 77.3 3.2 R16 11/9/13 10:20 25.0 1470 8.8 8.32 96.2 0.7 R17 11/9/13 8:55 23.0 1480 6.1 8.23 72.1 1.2 R18 11/9/13 8:35 23.5 1480 5.6 8.19 71.2 1.2 R19 11/9/13 9:40 24.2 1471 4.5 8.01 53.8 1.2 R20 11/9/13 9:30 24.1 1470 1.3 7.72 14.7 2.4 R21 10/9/13 10:10 24.6 1480 6.4 8.3 78.4 2.0 R22 10/9/13 9:30 24.4 1490 6.8 8.33 81.8 1.9 R23 10/9/13 10:00 24.6 1480 6.4 8.21 78 2.0 R24 11/9/13 9:10 23.8 1450 7.2 8.35 87.2 1.2 a Turbidity measured on 12/9/12, b turbidity measured on 10/9/13

Freshwater fish fauna of the Roper River 1 Appendix 4. Habitat, species richness (Sobs) and physical parameters at 24 sites in the Roper River.

Mid-channel Channel Depth velocity Site Branch Mesohabitat Hydraulic habitat Sobs width (m) (m) (m/s) R1 south billabong disconnected pool 4 6.0 0.5 0 R2 south main channel glide 5 24.5 4.1 0.02 R3 south main channel glide 7 24.3 1.6 0.05 R4 south backwater slackwater 7 4.7 0.5 0 R5 south main channel run 9 19.0 1.0 0.13 R6 south side channel run 6 4.0 0.4 0.19 R7 south main channel run 4 14.5 1.3 0.12 R8 south side channel run 8 5.5 0.5 0.02 R9 south side channel run 5 4.1 0.3 0.47 R10 north billabong disconnected pool 7 11.8 0.5 0 R11 north main channel connected pool 8 18.5 0.7 0 R12 north main channel run 4 4.6 0.1 0.24 R13 north side channel connected pool 8 4.8 1.0 0 R14 north main channel connected pool 6 4.8 1.0 0 R15 north billabong disconnected pool 5 3.0 0.3 0 R16 north main channel run/riffle 5 10.0 0.1 0.25 R17 north main channel connected pool 9 9.0 0.5 0 R18 north main channel connected pool 8 10.5 1.0 0 R19 north backwater slackwater 9 12.0 1.8 0 R20 north backwater slackwater 7 6.0 0.9 0 R21 south side channel run 8 5.0 1.0 0.12 R22 south backwater slackwater 10 4.5 0.7 0 R23 south main channel run 7 18.3 0.5 0.11 R24 north main channel glide 12 8.5 0.6 0.07

Freshwater fish fauna of the Roper River 2

Appendix 5. Habitat measurements at channel and transect scales at 24 bankside observation sites in the Roper River. Columns 2-7, channel; columns 8-14, transect.

. .

.

ara ara

arge arge arge

mall mall

arge arge

Vall. Sand

% %Ch %L woody debris %Sand %Other %Rock %Vall %Ch %L woody debris % #L woody debris #S woody debris Canopy cover Site %Rock R1 0 0 100 0 0 0 0 0 100 0 0 2 0 63.2 R2 100 0 0 0 0 0 40 0 60 0 53.6

R3 100 0 0 0 0 0 100 0 0 0 0 0 0 68.3 R4 0 0 100 0 0 0 0 0 100 0 0 1 0 85.6 R5 95 0 0 5 0 0 100 0 0 0 0 0 1 83.2 R6 45 55 0 0 0 0 45 55 0 0 0 0 0 82.7 R7 0 0 0 0 100 0 0 0 0 5 95 3 0 80.0 R8 0 30 70 0 0 0 30 70 0 0 0 0 0 77.9 R9 95 0 5 0 0 0 95 0 5 0 0 1 0 83.7 R10 5 0 95 0 0 0 10 0 90 0 0 0 0 44.7 R11 95 0 5 0 0 0 90 0 10 0 0 2 0 89.4 R12 90 0 0 0 0 10 100 0 0 0 0 0 0 58.7 R13 50 0 50 0 0 0 15 0 85 0 0 0 0 92.3 R14 50 0 50 0 0 0 15 0 85 0 0 0 0 92.3 R15 5 0 45 0 50 0 5 0 40 0 55 0 0 54.3 R16 100 0 0 0 0 0 100 0 0 0 0 0 0 26.4 R17 0 0 70 0 30 0 0 0 80 0 20 2 0 90.6 R18 0 0 70 0 30 0 0 0 100 0 0 3 0 77.9 R19 0 0 100 0 0 0 0 0 100 0 0 1 0 90.9 R20 0 0 100 0 0 0 0 0 100 0 0 1 0 28.4 R21 0 0 0 0 100 0 0 0 0 5 95 3 0 93.5 R22 0 0 95 5 0 0 0 0 95 5 0 3 1 76.9 R23 100 0 0 0 0 0 10 0 15 0 75 1 1 77.2 R24 0 0 10 0 90 0 0 0 10 0 90 1 1 88.5

Freshwater fish fauna of the Roper River 3 Appendix 6. List of fish specimens lodged with the Northern Territory Museum from field work conducted under this project in late 2013. Identifications provided by Dr Michael Hammer.

MAGNT Number Family Species Common name S.17575-001 6 Ambassidae Ambassis agrammus sailfin glassfish S.17575-002 3 Ambassidae Ambassis macleayi Macleay's glassfish S.17575-003 5 Melanotaeniidae Melanotaenia splendida inornata chequered rainbowfish S.17575-004 3 Apogonidae Glossamia aprion mouth almighty S.17575-005 2 Eleotridae Oxyeleotris lineolata sleepy cod S.17575-006 1 Terapontidae Hephaestus fuliginosus sooty grunter S.17575-007 1 Toxotidae Toxotes chatareus sevenspot archerfish S.17575-008 4 Atherinidae Craterocephalus stercusmuscarum fly-specked hardyhead S.17575-009 1 Gobiidae Glossogobius munroi square blotch goby S.17575-010 5 Gobiidae Glossogobius aureus golden flathead goby S.17575-011 2 Ariidae Neoarius berneyi highfin catfish S.17575-012 1 Ariidae Neoarius paucus shovelnose catfish S.17575-013 1 Soleidae Brachirus selheimi freshwater sole

Freshwater fish fauna of the Roper River 4