Factors driving life-histories in brown trout Salmo trutta exhibiting partial migration behaviours Pavel Mikheev A thesis submitted for the degree of Doctor of Philosophy in Zoology University of Otago Dunedin, New Zealand May 2019 Abstract The behaviors of some partially migratory salmonids, at both the among- and within- species levels, can be established early - on during their respective lives. For those species that have a plastic early life history in these regards, a variety of biological and environmental factors can result in some juvenile fish in a population to either stay resident within their natal streams or become migratory. This study examines the role of intraspecific competition as a trigger, either to remain resident or emigrate, for YoY (young-of-the-year) non-native (introduced) brown trout Salmo trutta found in a number of populations of selected natal streams in a large catchment in South Island, New Zealand. Brown trout are known to have the genetically- mediated flexibility leading to the potential establishment of a variety of within-population alternatives for migratory life-history outcomes (e.g., stay put, move out of the immediate area, become anadromous). The role of positive feedback loops generated by parents that either stay to live out their whole lives within their natal stream, or leave either to go to other freshwater environments (other streams, lakes) or the ocean, before spawning and producing viable offspring is examined in this study. This thesis provides strong evidence for the role of competition in initiating downstream movement of YoY brown trout populations. These are mechanisms leading to the establishment of feedback loops between the migratory or resident life-histories of adults and the density of juvenile fish while they are stream rearing. Competition amongst juveniles was assessed by estimating and comparing the demands for energy and space of a number of rearing populations of YoY fish and the capacity of study stream to provide food and space. Stream-carrying capacity was estimated using data on fish-habitat suitability, invertebrate drift, energetic demand and the trophic selectivity of YoY trout. In the lowland reaches of my study catchment the population densities of YoY fish in their natal streams were generally high. I found the intensity of competition within this category of natal streams, amongst the high-density populations of the offspring of migratory trout, to also be high. Anadromy was the dominant life-history strategy for adult brown trout in these low-gradient, lowland streams. Along the lowland reaches, positive associations between YoY loss rate (driven by both emigration and mortality) and intra-cohort competition, were observed. The intensity of competition amongst YoY cohorts was primarily determined by temperature-mediated energy restrictions rather than territorial limitations. In contrast, in the headwater streams which are inhabited by resident trout, the abundance of YoY juvenile fish was relatively low, and there was no evidence to indicate that competition influenced the loss rate of these fish. Hence, based on the densities, competition and self- ii thinning of YoY brown trout, this suggests that the majority of the recruitment across the catchment was driven by the high reproductive inputs into lowland spawning grounds from adults with migratory life-history traits. However, an analysis of the recruitment sources of fish using otolith microchemistry indicated that a high proportion of adults reproducing in the coastal part of the catchment originated from the upland part of the catchment. This indicates that populations of anadromous and potamodromous brown trout are likely comprised of individuals originated from throughout the entire catchment. Most notably, the geomorphology of the landscape limits the upstream migration and spawning distribution of large fecund migratory trout due to physical barriers. These results highlight the genetically-mediated life-history flexibility of brown trout and their ability to shift between either migratory or resident phenotypes at early life stages. This flexibility is sustained even in populations that have originated from a likely-narrow genetic pool of introduced lineages of brown trout. Considering current changes in global- climates, the findings of temperature-driven energetic restrictions on species distributions may be highly important for brown trout management and conservation in New Zealand and elsewhere. The observed flexibility in life-history traits and high straying from natal streams contributes to their ability to utilize a wide range of opportunities across catchments. iii To my wife Olga iv Acknowledgements I truly appreciate the strong support from my supervisors at all stages of this study. I would like to express the gratitude to my primary supervisor, Gerry Closs, for keeping his office open at all times, for being ready to discuss each question, as well as staying enthusiastic and positive. Many times, I came to him with ideas about the project, and his advice was always very helpful in following the right direction. This has been an amazing learning process and thank you, Gerry, for sharing your knowledge and experience with me. Without your support, this thesis wouldn’t be realized. I would like to thank my co-supervisor Christoph Matthaei for his amazing guidance in the project design, for organizing invertebrates’ data collection, statistical analysis and support in writing. Also, the quality of the work was much improved thanks to Travis Ingram recommendations who co-supervised me at the final stage of the work. Travis was always ready to talk and his advice in statistics and in organizing data chapters contributed a lot into my work. Rune Knudsen provided his opinion and very useful feedbacks which significantly improved the quality of the thesis. I want to thank lab members who helped me at various stages of the study. Many thanks go to Matt Jarvis for his help in all parts of the project. Thanks also go out to Sichen (Jeremy) Xu, Jason Augspurger, Fasil Taddese and Ewan Bakker for assistance in the field work. The design of this thesis would have required much-longer timeframes without the findings of the previous PhD students Esben Kristensen and Douglas Jones whom, unfortunately, I have not met in person. Thanks go out to Zoology Department staff members who taught me new skills, gave me good advice and assisted in the field and lab. I would also like to thank Kim Garret for teaching me key aspects of New Zealand fieldwork and electrofishing – without his experience and professionalism it would have been much harder for me to design and manage the project. I appreciate Nicky McHugh for her general support and advice in the lab. Nat Lim, and Sam Macaulay provided assistance in the fieldwork. Further, Ryan Easton, Jesse Wansbrough, Jolyn Chia and Marine Richarson all gave me advice in my writing of this thesis. Scott Jarvie and Luke Easton were instrumental in providing statistical analyses guidance. Aurelien Vivancos is also thanked for sharing his experience in aquatics and teaching me to film juvenile trout in the wild. I want to express my appreciation to the summer interns for assistance at the data collection and samples handling including: Jules Travert from Agrocampus Ouest in Rennes (France) for helping me in fry trap construction and in the field; Dylan Glaser from the University of Calgary (Canada); Julien Kriter Bréda from National School of Agronomy and Food Industries in Nancy (France); Pérandjali Latchoumy from the v School of Agricultural and Life Sciences in Toulouse (France); Johanna Kann and Teresa Bednarak from the Ruhr University in Bochum (Germany) for the assistance at the fieldwork and primary processing of samples in the lab. Input from three examiners greatly improved this thesis. I also truly appreciate the strong support of Otago Fish and Game Council staff members throughout this project; the contribution from Morgan and Helen Trotter and Steven Dixon, who helped me considerably in the understanding of New Zealand salmonid ecology and collection of the data, which completely differ from my previous experience, is acknowledged. Thanks also go out to to Niall Watson and Ian Hadland, who provided permission to collect brown trout samples. Special thanks are reserved for landowners for providing access to their properties in order to sample brown trout. The farmers were always very friendly and keen on talking about freshwater studies conducted by the University of Otago. This study was supported by the University of Otago Scholarship. As part of my studies I attended several fish conferences in New Zealand, Czech Republic, Canada and Spain during my PhD research; this would have been impossible without the financial support of the Division of Sciences of the University of Otago, Department of Zoology of the University of Otago, New Zealand Freshwater Sciences Society, Australian Society of Fish Biology, American Fisheries Society, and Ecology Research Group of the University of Otago. I appreciate Otago Animal Ethics Committee for its approval of the research, Otago Regional Council for providing Silverstream water flow data and Dunedin City Council for the access to Silverstream headwaters. Finally, I acknowledge and express my tremendous appreciation to my wife Olga who processed most of my samples, and for her patience and understanding. I cannot express enough thanks to my parents and children who are so important to me. All of you