Into the Wild Documenting and Predicting the Spread of Pacific Oysters (Crassostrea gigas) in Ireland Judith Kochmann (B.Sc., M.Sc.) The thesis is submitted to University College Dublin in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biology and Environmental Science Head of School: Dr. Thomas Gallagher Principal Supervisor: Dr. Tasman P. Crowe Doctoral Studies Panel Membership: Advisor: Dr. Mary Kelly-Quinn Chair: Dr. Jan-Robert Baars Dublin, August 2012 Table of Contents List of Tables ................................................................................................................................. v List of Figures ...............................................................................................................................vi Summary ..................................................................................................................................... vii Statement of Original Authorship......................................................................................... ix Collaborations .............................................................................................................................. x Acknowledgements ................................................................................................................... xi Chapter 1 General Introduction ............................................................................................ 1 1.1 Bioinvasions ................................................................................................................................. 1 1.1.1 Legislation ........................................................................................................................................... 1 1.1.2 Defining key concepts in invasion biology ............................................................................. 2 1.1.3 Stages of invasion ............................................................................................................................. 4 1.1.4 Factors affecting invasion success ............................................................................................. 5 1.1.5 Considerations for management ................................................................................................ 8 1.2 Methodologies for characterising and predicting invasions ...................................... 9 1.2.1 Models, observations and experiments................................................................................... 9 1.2.2 Genetic tools ..................................................................................................................................... 10 1.3 Aquaculture as a vector for invasive species................................................................. 11 1.4 Pacific oysters - a case of marine bioinvasion ............................................................... 12 1.5 Outline of study ........................................................................................................................ 18 Chapter 2 Environmental factors associated with the local establishment of Pacific oysters: modelling occurrence data from a coordinated sampling programme ................................................................................................................................. 20 2.1 Abstract ....................................................................................................................................... 21 2.2 Introduction .............................................................................................................................. 22 2.3 Methods ....................................................................................................................................... 24 2.3.1 Sampling programme ................................................................................................................... 24 2.3.2 Data Analysis .................................................................................................................................... 27 2.4 Results ......................................................................................................................................... 30 2.4.1 Distribution, densities and sizes of feral Pacific oysters ................................................ 30 2.4.2 Associations between oysters and environmental variables at the scale of sites (Phase 1) .............................................................................................................................................................. 30 2.4.3 Small-scale associations between oysters and habitat within sites (Phase 2) ...... 31 Tables .................................................................................................................................................................... 32 Figures .................................................................................................................................................................. 35 2.5 Discussion .................................................................................................................................. 38 Chapter 3 Effects of predation and macroalgae on survival and growth of juvenile Pacific oysters (Crassostrea gigas) ................................................................... 46 3.1 Abstract ....................................................................................................................................... 47 3.2 Introduction .............................................................................................................................. 48 3.3 Methods ....................................................................................................................................... 52 3.3.1 Experimental design, set up and sampling .......................................................................... 52 3.3.2 Crab trapping 2011 ........................................................................................................................ 55 3.3.3 Data analysis ..................................................................................................................................... 56 3.4 Results ......................................................................................................................................... 57 3.4.1 Survival ............................................................................................................................................... 57 3.4.2 Growth and Condition Index ...................................................................................................... 57 3.4.3 Supplementary analyses .............................................................................................................. 58 ii 3.4.4 Crab trapping 2011 ........................................................................................................................ 59 Tables .................................................................................................................................................................... 60 Figures .................................................................................................................................................................. 63 3.5 Discussion .................................................................................................................................. 67 3.5.1 Predation............................................................................................................................................ 67 3.5.2 Growth and Condition Index ...................................................................................................... 70 Chapter 4 Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species – a case study of Pacific oysters (Crassostrea gigas) .................................................................................................................. 74 4.1 Abstract ....................................................................................................................................... 75 4.2 Introduction .............................................................................................................................. 76 4.3 Methods ....................................................................................................................................... 77 4.3.1 Sample collection ............................................................................................................................ 77 4.3.2 Microsatellite data collection and analyses ......................................................................... 78 4.4 Statistical analyses .................................................................................................................. 79 4.5 Results ......................................................................................................................................... 80 4.5.1 Genetic variability .......................................................................................................................... 80 4.5.2 Population differentiation .......................................................................................................... 81 Tables ...................................................................................................................................................................