Refining biological monitoring of hydromorphological change in river channels using benthic riverfly larvae (Ephemeroptera, Plecoptera and Trichoptera). Anna Doeser November 2016 Submitted to Biological and Environmental Sciences School of Natural Sciences University of Stirling Scotland. For the degree of Doctor of Philosophy Supervisor: Prof. Nigel Willby 1 Statement of Originality I hereby confirm that this PhD thesis is an original piece of work conducted independently by the undersigned and all work contained herein has not been submitted for any other degree. All research material has been duly acknowledged and cited. Signature of Candidate: Anna Doeser Date 2 General Abstract Rivers and their catchments are under mounting pressure from direct channel modification, intensification of land use, and from a legacy of decades of channelisation. Recent legislation, in the form of the EU Water Framework Directive, places a greater emphasis on the management of water bodies as holistic systems, and includes the explicit consideration of hydromorphological quality, which describes the hydrologic and geomorphic elements of river habitats. These are defined specifically as hydrological regime, river continuity and river morphology. This appreciates that sediment and flow regimes, along with the channel structure, provides the 'template' on which stream ecological structure and function is built. Invertebrate fauna contribute significantly to the biodiversity of rivers, and often form the basis of monitoring river health. However much of the fundamental ecological knowledge base on the response of invertebrates to hydromorphological change needed to make informed decisions and accurate predictions, is either lacking, inadequate or contradictory. This thesis addresses some of the key potential shortcomings in recent bio-assessment that others have alluded to, but which have rarely been explored in the context of direct channel manipulations. By using two case studies of, realignment in a natural upland catchment, and flood protection engineering in an urban stream, this study investigates the sensitivity of hydromorphological impact assessment methods that rely on biodiversity patterns of benthic riverfly (Ephemeroptera, Plecoptera and Trichoptera) larva. This work employed widely used biomonitoring indices of benthic riverfly larva abundance, species richness, alpha and beta diversity, and community composition, applied over a range of spatial scales, in combination with spatially contemporaneous physical habitat data, to describe and explain community changes in response to disturbance, and patterns of natural variation. The effects of restoration were investigated using a high degree of sample replication within channels and across the wider catchment, as well as contrasting spring and autumn seasons. To assess change in a small urban channel, approaches that explicitly consider spatial elements of community data, using spatial eigenvectors analysis, were applied to spatially detrend community data and directly investigate spatial patterns. Restoration of the Rottal Burn was found to be successful in restoring habitat diversity and geomorphic processes, and in turn increasing reach scale species richness and beta diversity through the gradual arrival of rare and specialist taxa into novel habitats. Catchment scale replication revealed high variation in diversity indices of modified and undisturbed streams, and 3 a strong temporal pattern related to antecedent flow conditions. Channels with greater habitat heterogeneity were able to maintain high gamma diversity during times of high flow stress by providing a number of low flow refuges along their length. The urban Brox Burn had surprisingly high riverfly richness and diversity driven by small scale hydraulic heterogeneity, created by bed roughness resulting in a range of microhabitats. Riverfly community responses to direct channel dredging could not be detected by measurements of average richness and diversity, however distinct changes were seen in gamma diversity, the identity of community members and their arrangement among sample patches. Impacts of sediment pollution release due to engineering were short lived and apparently had little detrimental impact on biodiversity. Strong spatial patterns of community assembly on the stream bed were uncovered, relating to longitudinal, edge and patchy patterns. Significant habitat drivers of community composition were confounded by high amounts of spatial autocorrelation, especially hydraulic variables. Due to the strongly physical and spatial nature of hydromorphological disturbance, turnover of species between sample locations at a range of scales, and the spatial arrangement of habitats and communities is of more use for detecting these types of subtle changes compared to mean richness or diversity. These findings have implications for the targeting of resources for monitoring of restoration, or engineering disturbances, in order to be sensitive to hydromorphological change. Efforts should target the main area of natural variability within the system, either replicating sampling in time or space to distinguish effects of impact. Spatial patterns, measures of beta diversity and species identity can be better exploited to identify systems with functioning geomorphological processes. Channel typologies proved misleading, and quantification of habitat and selection of control sites using multiple pre-defined criteria should be carried out. Studies of restoration operations and engineering impacts provide considerable opportunities for advancing our knowledge of the mechanisms that drive community response under a range of conditions to improve impact detection. 4 Acknowledgements Special thanks to my supervisor Professor Nigel Willby, who has been a constant source of encouragement and fruitful river "nerd-out" sessions over the past four years. This project would not have been possible without the generous funding from SEPA, and strong initial direction and enthusiastic support from Chris Bromley. Additional funding support through Stirling University Impact Studentship was also gratefully received. Thanks also to Prof. Dave Gilvear for providing a friendly welcome, early support and local allotment (sadly neglected). Many thanks to the assistance from Marshall Halliday and particularly Steve Hawkins of the Esk Rivers and Fisheries Trust for showing me the lay of the land in Glen Clova. Also the enthusiastic permission of the Rottal Estates landowner Dee Ward. Thanks to my fellow, past and present colleagues at the Number 1 Freshwater Detective Agency: Alan Law, Colin Bull, Charlie Perfect and Alex Seeney. Thanks to Roni Balfour, Scott Jackson and Helen Ewen for technical and logistical support. Also to Tim Paine for taking the time to get me looping with R, which has saved me many hours or work, and now I cannot stop. My thanks to those brave people who assisted in the lab and the field over years either for love or money: Lois Campbell, Megan Layton, Mellissa Shaw, David Eastwood, Ross Hepburn, Adam Welsh, Catherine Gibson-Pool, Renee Hermans, Junyao Sun. My special thanks David García Martínez and Clara Gajas Roig for spending a summer wading in the Broxburn, at least I took you to Glen Clova too! To my treasured Toothless and Abrosius, who have brought me great happiness and much needed exercise in the beautiful scenery of Stirling through stressful times (my bikes..). Finally, to my parents Kathy and Bernie, for always encouraging me to do what makes me happy and never doubt what I could achieve. Also to my brother Dr James Doeser; there may have been a small aspect of sibling rivalry prompting me to pursue this PhD, and my grandma Renee, who supported all my academic endeavours. 5 Table of Contents Statement of Originality ................................................................................................................ 2 General Abstract ........................................................................................................................... 3 Acknowledgements ....................................................................................................................... 5 List of Figures ............................................................................................................................. 10 List of Tables .............................................................................................................................. 18 Chapter 1 - General Introduction ................................................................................................ 22 1.1 River systems in modern society ...................................................................................... 22 1.2 Knowledge gaps in stream ecology .................................................................................. 24 1.3 Study aims and overview .................................................................................................. 26 Chapter 2 – Measuring and evaluating success of a restoration project using benthic riverfly larvae, implications for monitoring ............................................................................................. 29 2.1 Introduction ...................................................................................................................... 29 2.1.1 History of river modification ..................................................................................... 29 2.1.2 The fluvial landscape ...............................................................................................