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University of Southampton Research Repository University of Southampton Research Repository Copyright © and Moral Rights for this thesis and, where applicable, any accompanying data are retained by the author and/or other copyright owners. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis and the accompanying data cannot be reproduced or quoted extensively from without first obtaining permission in writing from the copyright holder/s. The content of the thesis and accompanying research data (where applicable) must not be changed in any way or sold commercially in any format or medium without the formal permission of the copyright holder/s. When referring to this thesis and any accompanying data, full bibliographic details must be given, e.g. Thesis: Author (Year of Submission) "Full thesis title", University of Southampton, name of the University Faculty or School or Department, PhD Thesis, pagination. Data: Author (Year) Title. URI [dataset] UNIVERSITY OF SOUTHAMPTON FACULTY OF ENGINEERING AND THE ENVIRONMENT Centre for Environmental Sciences Civil, Maritime, and Environmental Engineering and Science Quantification of the collective response of fish to hydrodynamics for improving downstream fish passage facilities by Jasper de Bie Thesis for the degree of Doctor of Philosophy April 2017 UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF ENGINEERING AND THE ENVIRONMENT Civil, Maritime and Environmental Engineering and Science Thesis for the degree of Doctor of Philosophy Quantification of the collective response of fish to hydrodynamics for improving downstream fish passage facilities Jasper de Bie Migrating freshwater fish species are limited in their longitudinal movements due to barriers representing anthropogenic water resource management. Technologies, such as physical screens, designed to mitigate the effects of these obstacles on downstream migrating fish, are currently not functioning to a high standard, due to a lack of understanding of the response of fish to hydrodynamics encountered at screens. Furthermore, collective behaviour is often not considered in this context. This thesis addresses these issues through experimental studies conducted in recirculating flumes. There is a lack of understanding on the fundamental interactions that underlie collective fish movement in lotic conditions. To address this, the shoal structure and interaction rules of pairs of Eurasian minnow, Phoxinus phoxinus, were studied under flowing conditions and standing water, and energy expenditure in terms of drag modelled using CFD software. Results indicate that flow promotes shoaling but induces a change in shoal structure due to individuals aiming to maximize information transfer rather than exploiting energetic benefits. Besides economic important species, such as salmonids, the wider fish community is often ignored in fish screening research. Several experiments were carried out to assess the performance of bar racks and wedge-wire screens for downstream moving small groups of chub, Squalius cephalus, and barbel, Barbus barbus, under two discharge regimes. A horizontal alignment of bars was, for the first time, compared to the traditionally used vertical alignment in terms of hydrodynamics created at the screen and performance. Horizontal and vertical bar racks did not differ in the flow fields they induced, with mean flow primarily directed going through the racks. Avoidance responses were stronger in chub than barbel, but for both species this resulted in high numbers of entrained fish, regardless of rack configuration or discharge regime. Wedge-wire screens with a small bar spacing to eliminate entrainment seemed efficient in guiding chub, although strong avoidance behaviour was observed. Vertical wedge-wire screens induced higher sweeping velocities along the screen, however the horizontal one under low discharge produced highest guidance efficiency. The experiments confirm the importance of avoidance behaviour to hydrodynamics in the context of successfully fish screening. Shoal cohesion was weak for both species, and warrants further research into identifying the factors responsible. The results presented in this body of research are an important step to a better understanding of how fish respond to flow, which can have implications for collective modelling of animal movements in complex environments. Furthermore, it helped improve screen design criteria for the fish species used. In turn, this will help maintaining healthy fish populations that can benefit freshwater ecosystems. Table of Contents Table of Contents ................................................................................................... i List of Tables ......................................................................................................... v List of Figures ..................................................................................................... vii DECLARATION OF AUTHORSHIP ..................................................................... xv Acknowledgements .......................................................................................... xvii Glossary of Terms ............................................................................................. xix A: Fish families ................................................................................................. xix B: Fish species ................................................................................................. xxi C: General terms ............................................................................................ xxiii Chapter 1: Thesis Introduction ..................................................................... 1 1.1 Introduction ................................................................................................ 1 1.2 Thesis aim and objectives .......................................................................... 4 1.3 Thesis overview ......................................................................................... 4 Chapter 2: Literature Review ......................................................................... 7 2.1 Benefits of group formation ........................................................................ 7 2.2 Costs of group formation .......................................................................... 10 2.3 Terminology ............................................................................................. 11 2.4 Self-organisation in groups ....................................................................... 13 2.5 Downstream fish passage solutions ......................................................... 15 2.5.1 Design Criteria ............................................................................. 18 2.5.2 Evaluation of screen performance ............................................... 20 2.5.3 Factors limiting efficiency ............................................................. 22 2.6 Fish behaviour and hydrodynamics .......................................................... 24 2.7 Summary .................................................................................................. 31 Chapter 3: General Methodology ................................................................ 35 3.1 Flume facilities ......................................................................................... 35 3.2 Video analysis and tracking ...................................................................... 38 3.3 Hydrodynamics ........................................................................................ 38 3.4 Fish husbandry and handling ................................................................... 39 i 3.5 Test species ............................................................................................. 41 3.5.1 Eurasian minnow ......................................................................... 41 3.5.2 Chub ............................................................................................ 41 3.5.3 Barbel .......................................................................................... 42 Chapter 4: Collective fish behaviour in response to flow ......................... 45 Summary .......................................................................................................... 45 4.1 Introduction .............................................................................................. 46 4.2 Materials and Methodology ...................................................................... 49 4.2.1 Experimental set-up ..................................................................... 49 4.2.2 Experimental procedure ............................................................... 51 4.2.3 Tracking and behavioural analysis............................................... 52 4.2.4 Numerical analysis ....................................................................... 55 4.2.5 Statistics ...................................................................................... 59 4.3 Results ..................................................................................................... 60 4.4 Discussion ................................................................................................ 69 4.5 Conclusions .............................................................................................. 73 Chapter 5: Effectiveness of horizontally and vertically oriented bar racks to guide juvenile chub (Squalius cephalus) and barbel (Barbus barbus) under
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