Drivers of Stream Fish Assemblages and Trophic Interactions A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy In Ecology At the University of Canterbury By Kevin Marshall Fraley School of Biological Sciences University of Canterbury Christchurch, New Zealand 2018 For my father, John Fraley “Swift or smooth, broad as the Hudson or narrow enough to scrape your gunwales, every river is a world of its own, unique in pattern and personality. Each mile on a river will take you further from home than a hundred miles on a road.” -Bob Marshall Table of Contents Abstract ...................................................................................................................................... 1 Chapter One: Introduction ......................................................................................................... 3 Chapter Two: Responsiveness of fish mass–abundance relationships .................................... 15 Appendix 2A: Supplemental table and figures .................................................................... 47 Appendix 2B: Single-pass electrofishing methods verification........................................... 51 Chapter Three: Big Impacts from small abstractions .............................................................. 57 Appendix 3A: Supplemental table and figures .................................................................... 86 Chapter Four: Variable influences on fish trophic position ..................................................... 91 Appendix 4A: A. australis fin clip to muscle tissue regression ......................................... 115 Appendix 4B: Verification of stable isotope baseline ....................................................... 116 Chapter Five: Habitat effects on community biomass and trophic structure ......................... 121 Appendix 5A. Rationale for δ15N predicted relationships ................................................. 146 Appendix 5B. Rationale for community biomass predicted relationships ........................ 148 Chapter Six: General discussion ............................................................................................ 151 Acknowledgements ................................................................................................................ 163 References .............................................................................................................................. 167 Appendix A: Ngāi Tahu Letter of Support ............................................................................ 189 Abstract Human and environmentally-driven changes in flood disturbance, habitat size, and land cover can affect fish assemblages in streams. However, it is important to understand the mechanisms underlying these so that resource managers can minimize the effects of detrimental perturbations. This is particularly vital for streams that contain endemic, at-risk taxa or species of recreational and economic importance. Therefore, developing functional measures of fish assemblages which summarize energy flow and trophic pathways (e.g., food-chain length) could be useful to quantify the effects of habitat changes on aquatic communities. To address this, I surveyed thirty headwater Canterbury, New Zealand streams to evaluate fish mass–abundance relationships (size spectra) and stable isotope metrics (food-chain length and carbon range) as functional measures of aquatic ecosystems and their response to the aforementioned habitat factors. I found that these metrics were responsive to increasing habitat size (food chains lengthened), flood disturbance (carbon range and mass–abundance slopes decreased), and riparian land cover types, proving effectual as integrative measures of aquatic ecosystems. Next, using these newly-vetted metrics, I assessed the effects of small-scale surface water abstractions on fish assemblages and community trophic structure. I found decreased habitat size downstream of water abstractions was associated with lower abundances of large-bodied fishes, shorter food chains, and predatory release for sensitive, small-bodied native taxa. I then quantified the effects of habitat size and flood disturbance on theorized relationships between fish body mass and trophic position. Here, I found negative influences of these habitat factors on the trophic position of individual fish species, confirming that environmental factors can be as important as fish body size in determining trophic height. 1 Finally, I identified the specific mechanisms regulating invertebrate and fish trophic height, as well as community biomass through structural equation modelling. I found that flood disturbance negatively affected both the trophic height and biomass of large-bodied non- native salmonids. Additionally, habitat size and land cover types variably influenced the trophic height of small-bodied native fishes and invertebrates, along with algal, allochthonous, invertebrate, and fish biomass. Overall, my research has advanced understanding of how flood disturbance, habitat size, and riparian land cover affect freshwater fishes and community food webs through modulation of both trophic structure and fish body size. When used in-tandem, fish mass–abundance relationships and stable isotope-derived food-web metrics will be useful measures for monitoring, mitigating, and rehabilitating aquatic communities in the face of pressures caused by land-use change, flow alteration, and non-native species. Thus, these metrics could provide additional tools to inform appropriate management decisions. 2 Chapter One Introduction A beautifully-dappled brown trout caught in a New Zealand backcountry river. 3 Key Influences on Stream Ecosystems Understanding how abiotic and biotic factors affect stream ecosystems and fish assemblages is useful for investigating effects of human habitat alteration on aquatic communities. Habitat conditions such as temperature and habitat size affect stream fish feeding behaviour, diet, energy budgets, and trophic structure (Post et al. 2000; Arim et al. 2007). Additionally, factors such as stream size, flood disturbance, riparian land cover, and non-native predator presence influence fish assemblages (McHugh et al. 2010). However, the effects of these habitat components, particularly differing land cover type, are not well- quantified or understood. Therefore, I have reviewed and explored several of the most influential drivers for New Zealand stream fishes in the following sections, and in my doctoral research presented in this thesis. Stream flow and flood disturbance In most cases, unmodified flow maximizes connectivity of stream networks for broad- scale energy transfer and subsidies, natural flow variability and flooding, and downstream dispersal of aquatic invertebrates (Bunn & Arthington 2002; Postel & Richter 2012; Datry et al. 2014). In many streams, natural flood disturbance regimes are thought to structure fish assemblages and food webs (Wootton et al. 1996; Davey & Kelly 2007; McHugh et al. 2010). This is because flood-prone streams are harsh environments, typically having lower standing stocks of basal resources due to stream bed shift during floods. This may be beneficial for native taxa however, which are adapted to cope with extremes in flow (Leprieur et al. 2006), which I have investigated further in this thesis. However, natural flow fluctuations are often threatened by human modification and manipulation of watercourses (Poff et al. 1997; Lytle & Poff 2004), and because some of the most important influences on streams revolve around flows, flow alteration by humans is a major concern. Therefore, I focused heavily on investigating the effects of flood disturbance on stream fish assemblages in this thesis by 4 comparing streams across a gradient from flood-prone, braided rivers to relatively stable spring creeks. Habitat size Flooding disturbance encapsulates one aspect of stream flow regimes, and is related to fluctuations in discharge, which in turn influences the size of aquatic habitats. Globally, stream food webs are highly dependent on water levels and flow to maximize availability of habitats for biota (Allan & Castillo 2007; Davies et al. 2014), with dewatered streams typically displaying shrunken aquatic spaces. The size of habitats available for freshwater fishes can be important in determining abundance, biomass, and possibly trophic structure within assemblages (McHugh et al. 2010; Sabo et al. 2010). Although it has been found that increased habitat size does not increase per unit area productivity in New Zealand streams (McIntosh et al. 2018), larger habitats should have increased total biomass of fish per unit stream length because there is more productive space in a larger habitat that should lead to a greater abundance of prey (Vander Zanden et al. 1999). However, there is some debate about whether habitat size influences trophic structure of stream communities (Post et al. 2000; Sabo et al. 2010). If habitat size is an important influence on food-web structure, human- caused habitat size reduction from damming, water abstraction, and diversion in streams may be problematic (Falke et al. 2011), likely affecting fish assemblages (McHugh et al. 2015). In New Zealand, the most common type of flow modification that results in habitat size reduction is water abstraction for agricultural purposes. Therefore, I examined both the effects of natural habitat size gradients (ranging from streams that were mere trickles to large,