Surveying rare fishes in rivers

By Brendan Ebner, Tropical Landscapes Joint Venture, CSIRO Land & Water and TropWATER, James Cook University, Townsville, QLD.

Wet tropics stream

A Wet Tropics stream just waiting to be snorkelled

Freshwater ecosystems are some of the most threatened on the planet. Freshwater fish are particularly imperilled: worldwide, 46% of all fish species are considered to be at risk of extinction by the International Union for the Conservation of Nature. It’s a very sobering thought that things are in such a bad state. But scientists, conservationists and natural resource managers are working hard to try to turn this around. One of the fundamental needs for all of this work is to determine the population size and distribution of fishes in rivers, and especially those fishes that are rare. Common ones are relatively easy to find, as any fisher will tell you. But it is the rare species – and these are often the ones that are at greatest risk of extinction – that we want to know most about, but are the hardest to find. It is an issue that fish ecologists have been grappling with for years. Interestingly, progress is being made, and increasingly includes a mix of low-tech and high-tech solutions.

Rare species defined

Rare fishes commonly feature on threatened species lists, since small population size and range are considered to increase vulnerability to extinction (Caughley and Gunn 1996). Generally, rare species have low abundance and/or a small range (Gaston 1994). In the absence of precise knowledge, relative abundance of species or estimates of range are typical proxies for rarity. This imperfect state of knowledge results in instances of pseudorarity – when a species is thought to be rare when it isn’t – and non-apparent rarity – when a species is thought to be common or widespread when it isn’t (Gaston 1994).

Bloomfield night perch

A Wet Tropics stream just waiting to be snorkelled

The abundance and distribution of riverine fishes can be challenging to determine. Riverine fishes are rarely randomly or evenly spread-out in rivers. Typically, they occur in aggregations along the main-stem of a river and in off-channel habitats, and this can change seasonally and year-to-year (Humphries and Walker 2013). Rare species can also be sparsely distributed, and this means they are unlikely to be collected in large catchments using normal survey techniques and amounts of effort (e.g. Hughes et al. 2002). Models are sometimes used to deal with poor detection of rare species, but models are only useful up to a point, because of problems with testing them adequately (Kunin and Gaston 1993, Gaston 1994).

Species detection bias in fish assemblage surveys

Comparisons of the species-specific detection arising from applying different survey techniques can be very useful when trying to find rare fish species, especially in large rivers, (e.g. Ebner and Morgan 2013, Weyl et al. 2013). Although this gives some sense of which technique or combination of techniques is likely to reveal the maximum number of species, it falls short of estimating how many individuals of each species may be present at a reach. It therefore can become no more than a species richness audit, which has limited utility for conservation and management (see Nabhan 1995 for a full explanation).

Relative abundance (% composition) and presence/absence are the most common ways to describe riverine fish assemblages, because it is far more costly to attempt to estimate absolute abundance of species directly, or to determine the relative detectability of each species. The cost and logistics of such exercises also become increasingly challenging with river size. Pusey and colleagues (1998) provide an informative validation of single-pass back-pack electrofishing based on multiple-pass depletion sampling of fishes in wadable streams in tropical Australia. Similarly, Faragher and Rodgers (1997) conducted depletion sampling in the context of non-wadable rivers in temperate Australia. In reaches of small streams, species detection has sometimes been calibrated by using rotenone (localised poisoning of the entire fish assemblage). However, for ethical and legal reasons, this approach should be conducted infrequently, and perhaps only for the eradication of pest species (e.g. Lintermans 2000, Weyl et al. 2013).

As I have said, attempts to determine absolute density of species in temperate and tropical Australian rivers are relatively uncommon, and this does little to dispel problems of pseudorarity and non-apparent rarity. For logistical reasons, these attempts are usually confined to small sections of river or stream that are comparable in size to those used in far more common relative abundance and presence/absence sampling (e.g. Faragher and Rodgers 1997, Pusey et al. 1998). The work of Lyon, Bird and colleagues (Bird et al. 2014, Lyon et al. 2014), goes some way to working beyond the constraints of a reach. These studies used a mark-recapture approach to estimate absolute abundance at a reach, and coupled this with a movement study (using telemetry) to determine when individual fish were either in, or outside, the study reach. Specifically, the probability that individual fish are present within a reach that is being surveyed was known.

This leads us to the very real challenge of surveying fishes along substantial lengths of river (see also: Fausch et al. 2002, Cao et al. 2001).

Continuous surveys along river reaches

There is a relatively rich literature from the Northern Hemisphere (and primarily North America) where substantial survey effort has been applied along continuous lengths of river. Numerous studies document patterns of fish assemblage distribution and establish single-pass sampling effort requirements for detecting single species, species richness, and diversity (e.g. Lyons 1992, Hughes et al. 2002). In many cases, boat or back-pack electrofishing is the technique of choice, depending on whether the streams are wadable or not. One of the more interesting findings from this line of enquiry, has been the realisation that there are river-specific patterns in distribution of fish diversity that require different levels of survey effort to achieve representative sampling (e.g. Cao et al. 2001).

In Australia, this issue has barely received any attention. More than a decade ago, researchers from the Australian Capital Territory (ACT) government, New South Wales Fisheries and the University of Canberra planned to collect a large-bodied threatened species, the Bluenose cod (Maccullochella macquariensis), from a river reach of the Murrumbidgee River, near Narrandera, for a radio-tracking study. This reach was considered relatively unusual at that time because stocking had led to a high relative abundance of Bluenose cod in the Murrumbidgee River, to the point that anglers were complaining that this was all they would catch. Nevertheless, the experience of one member of our team (Ian Wooden) had us expecting to have to boat electrofish along several kilometres of the river over weeks to attain our target sample of 30 Bluenose cod (of sufficient body size) for radio-tagging.

Bluenose cod

A Bluenose cod, Maccullochella macquariensis: the centre of attention for a radio-tracking and spin-off electrofishing study in the Murrumbidgee River (Photograph: Jason Thiem)

We seized on the opportunity, and decided to maintain detailed records of fish assemblage catch data to enable post hoc subsampling of the unusually large dataset relating to a single reach. While the resultant manuscript only narrowly made it through peer review (largely because we only had data from a single reach that prevented us from making any defensible generalisations in time or space beyond), it did provide for some interesting preliminary insights into what standard single pass electrofishing would reveal of the fishes in that reach (Ebner et al. 2008). Specifically, it showed that a number of species, including some that were not rare within the reach, could remain undetected within a typical length of river surveyed at the conventional scale (e.g. 1 km), because these species were patchily distributed longitudinally. It also exposed a more predictable result: that rare species were highly unlikely to be detected by standard single-pass survey effort.

Fish assemblages in short, steep coastal streams

After our team from the ACT Government successfully used snorkelling as a technique to rapidly survey threatened Macquarie perch (Macquaria australasica) nursery grounds in an upland temperate stream (Broadhurst et al. 2012), and following my relocation to the Australian Wet Tropics, where clear streams abound, it seemed sensible to snorkel and survey fish assemblages along kilometres of streams. Currently, in conjunction with colleagues (Paul Thuesen and James Donaldson), I am in the process of collecting data along continuous stretches of small tropical streams, with a view to investigating longitudinal and altitudinal patterns in goby (small benthic fishes) distribution. Preliminary results have been promising (Ebner et al. 2011, Thuesen et al. 2011). Using such techniques, we hope to step a little closer to attaining stream-specific sampling strategies akin to those developed in North America (e.g. Cao et al. 2001, Hughes et al. 2002).

Clearly, datasets spanning continuous lengths of stream are not easy to come by; most notably in large lowland rivers. Nevertheless, progress in multiple rivers with different fish assemblages should in time enable us to appreciate fish assemblage structure, the artefacts of our various survey and sampling strategies, and the distribution of rare species in Australian rivers. Environmental DNA, or eDNA, also holds some promise in this regard.

For now, the small tropical streams that I work in are useful model systems, owing to the practicality of surveying fish assemblages along the full extent of these systems, and the suitability of snorkelling to record a conspicuous diurnal fauna. There are many fascinating offshoots of this work, not the least of which is wondering how the hell some of the rare and highly localised species make do ecologically (and even how/why they may have evolved). Another relevant issue is how the rare and common species interact, and if they are playing by a different set of rules to one another (Kunin and Gaston 1993).


Directly counting fishes by snorkelling (left), facilitates identification of longitudinal patterns in distribution of conspicuous fishes, including highly aggregated and narrow niche specialist species including the red-tailed cling goby, Sicyopus discordipinnis (right), in small tropical streams.


Inevitably, the widespread use of relative abundance data pertaining to riverine fish assemblages shapes our view of the structure of these assemblages. Two important considerations are: a) checking the relative detection of species against true density estimates, or at least cross checking detection by different survey techniques; and b) expanding search areas beyond small numbers of small reaches. It follows that developing rapid survey techniques to achieve comprehensive understanding of the spatial distribution of fish assemblages in large river catchments is a Holy Grail that will integrate knowledge of rare and common species at the assemblage level.


The content of this article emerged from countless conversations and experiences with others including but not limited to Mark Lintermans, Ian Wooden, Jason Thiem, Simon Linke, Ben Broadhurst, David Morgan, Paul Thuesen, Steve Beatty, Philippe Keith and David Boseto. Earlier drafts were improved by comments from Shaun Meredith and Adam Kerezsy, and ultimately the editing of Paul Humphries. The FRDC is acknowledged for funding the original electrofishing study at Narrandera. Snorkel based surveys and spatial modelling of fishes continue to be championed in the grossly under-resourced but scintillating streams of the Wet Tropics through the efforts of James Donaldson.

References: Caughley, G. and Gunn, A. (1996). Conservation biology in theory and practice. MA: Blackwell Science. Bird, T., Lyon, J., Nicol, S., McCarthy, M., & Barker, R. (2014). Estimating population size in the presence of temporary migration using a joint analysis of telemetry and capture-recapture data. Methods in Ecology and Evolution 5, 615–625. Broadhurst, B. T, Ebner, B. C. and Clear, R. C. (2012). A rock-ramp fishway expands nursery grounds of the endangered Macquarie perch Macquaria australasica. Australian Journal of Zoology 60, 91–100. Cao, Y., Larsen, D. P., & Hughes, R. M. (2001). Evaluating sampling sufficiency in fish assemblage surveys: a similarity-based approach. Canadian Journal of Fisheries and Aquatic Sciences58, 1782–1793. Ebner, B. C. & Morgan D. L. (2013). Using remote underwater video to estimate freshwater fish species richness. Journal of Fish Biology 82, 1592–1612. Ebner, B.C., Thiem, J.D., Gilligan, D.M., Lintermans, M., Wooden, I.J., Linke, S., (2008). Estimating species richness and catch per unit effort from boat electro-fishing in a lowland river in temperate Australia. Austral Ecology 33, 891–901. Ebner, B. C., Thuesen, P. A., Larson, H. & Keith, P. (2011). A review of distribution, field observations and precautionary conservation requirements for sicydiine gobies in Australia. Cybium 35, 397–414. Faragher, R. A. and Rodgers, M. (1997). Performance of samplinggear types in the New SouthWales rivers survey. In: Fish and Rivers in Stress:The NSW Rivers Survey (eds J. H. Harris & P. C. Gehrke) pp. 251–68. NSW Fisheries Office of Conservation and the Cooperative Research Centre for Freshwater Ecology, Cronulla. Fausch, K. D, Torgersen, C. E, Baxter, C. V, and Li, H. W. (2002). Landscapes to riverscapes: bridging the gap between research and conservation of stream fishes. BioScience 52, 483– 98. Gaston, K. J. (1994). Rarity. Chapman and Hall: Melbourne. Hughes, R. M., Kaufmann, P. R., Herlihy, A. T. et al. (2002). Electrofishing distance needed to estimate fish species richness in raftable Oregon Rivers. North Amercian Journal of Fisheries Management 22, 1229–40. Humphries, P., and Walker, K. (2013). Ecology of Australian freshwater fishes. CSIRO Publishing: Clayton. Lintermans, M. (2000). Recolonization by the mountain galaxias Galaxias olidus of a montane stream after the eradication of rainbow trout Oncorhynchus mykissMarine and Freshwater Research 51, 799–804. Lyon, J. P., Bird, T., Nicol, S., Kearns, J., O’Mahony, J., Todd, C R., Cowx, I. G., and Bradshaw, C. J. A. (2014). Efficiency of electrofishing in turbid lowland rivers: implications for measuring temporal change in fish populations. Canadian Journal of Fisheries and Aquatic Sciences 71, 878–886. Lyons, J. (1992). The length of stream to sample with a towed electrofishing unit when fish species richness is estimated. North Amercian Journal of Fisheries Management 12, 198–203. Kunin, W. E. and Gaston, K. J. (1993). The biology of rarity: patterns, causes and consequences. Trends in Ecology & Evolution 8, 298–301. Nabhan, G. P. (1995). The Danger of reductionism in biodiversity conservation. Conservation Biology 9, 479−481. Pusey, B. J., Kennard, M. J., Arthur, J. M., and Arthington, A. H. (1998). Quantitative sampling of stream fish assemblages: Single‐vs multiple‐pass electrofishing. Australian Journal of Ecology 23, 365–374. Thuesen, P. A., Ebner, B. C., Larson, H., Keith, P., Silcock, R. M., Prince, J. and Russell, D. J. (2011). Amphidromy links a newly documented fish community of continental Australian streams, to oceanic islands of the West-Pacific. PLOS One 6: e26685. Weyl, O. L. F., Ellender, B. R., Woodford, D. J., and Jordaan, M. S. (2013). Fish distributions in the Rondegat River, Cape Floristic Region, South Africa, and the immediate impact of rotenone treatment in an invaded reach. African Journal of Aquatic Science 38, 201–209.

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