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Invasion and Evolutionary History of a Generalist Fish Parasite Salma Sana

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Invasion and Evolutionary History of a Generalist Fish Parasite Salma Sana Invasion and evolutionary history of a generalist fish parasite Salma Sana A thesis submitted in partial fulfilment of the requirements of Bournemouth University for the degree of Doctor of Philosophy December 2016 Copyright Statement This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and due acknowledgement must always be made of the use of any material contained in, or derived from, this thesis. 2 Acknowledgements Firstly, I would like to express my deepest gratitude to Allah who gave me the strength to complete this work. Thank you to my supervisors: Tiantian Zhang who in the first place provided me this opportunity and her guidance and support throughout the project and my day to day supervisor Demetra Andreou who has been a constant support over the last three years. Thank you for your invaluable guidance and help throughout this project. I would also like to thank Emilie Hardouin for her help with the DNA softwares and my viva examiners Rob Britton and Trenton Garner for their valuable feedback and advice. Dr Richard Paley who always has kindly provided RA spores and cultures whenever there has been a mishap at my end. I am also grateful to my parents and family for their love and support at every step of my life. I can’t thank you enough for all you have done for me. Last- but in no way least- to Ata without his support and sacrifice I would have never been able to complete my PhD and Kazeem who makes me feel proud every day. 3 Authors declaration I confirm that the work presented in this thesis is my own work, with the following exceptions: Chapter 4: The work presented in this chapter was in collaboration with the Environment Agency. The fish were sampled and dissected at Environment Agency and samples (organ tissue) were provided for processing. Histopathology was also performed by the Environment Agency. Chapter 5: Water sampling pre-Pseudorasbora parva eradication (2013) by Phil Davison. 4 Salma Sana Invasion and evolutionary history of a generalist fish parasite Abstract The introduction of non-native species can lead to the introduction of non-native parasites to their introduced range which can pose significant risk to native biodiversity. The cyprinid fish species, Pseudorasbora parva, is a well-studied example of accidental introduction to a new range; it has been accidentally introduced from China to Europe. Pseudorasbora parva has been hypothesized to have also introduced the generalist fish pathogen Sphaerothecum destruens to Europe which has been identified as a potential threat to European fish biodiversity. Due to the management implications associated with the parasite’s status (native or non-native), this work aimed at determining the S. destruens origin and distribution across its native and non-native P. parva populations, whilst also developing eDNA detection methods in order to assess the efficacy of P. parva eradication as a viable control measure for S. destruens. Due to the unique taxonomical position of S. destruens in tree of life, its mitochondrial DNA evolutionary history was also investigated to better decipher its phylogenetic position. Sphaerothecum destruens presence was confirmed in 90 % of the P. parva sampled populations from China, with a maximum prevalence of 10 %. Furthermore, the phylogenetic and demographic analysis of both the host and the parasite support the hypothesis that S. destruens has been introduced to Europe through the accidental introduction of its reservoir host P. parva. The non-native status of S. destruens in Europe has important management implications for the parasite. Furthermore, S. 5 destruens was detected in 50 % of the P. parva samples from 7 populations in the UK and identified new potential hosts for S. destruens in the wild including chub Squalius cephalus, dace leuciscus, roach Rutilus rutilus and brown trout Salmo trutta. The environmental DNA method detected S. destruens in water samples from a P. parva eradicated site 2 years after its eradication which emphasizes that preventive measures against pathogen expansion should be implemented. The phylogenetic tree based on mitochondrial derived protein sequences revealed an interesting position for S. destruens as a sister group to Filasterea and Choanoflagellate and Metazoa group and it has the most derived mitochondrial genome among Choanozoa. 6 Table of Contents Copyright Statement ..................................................................................................... 2 Acknowledgements ....................................................................................................... 3 Authors declaration ....................................................................................................... 4 Abstract ........................................................................................................................ 5 Table of Contents .......................................................................................................... 2 List of figures ............................................................................................................... 6 List of Tables .............................................................................................................. 13 Chapter 1 .................................................................................................................... 15 1.1 The Healthy Host, Pseudorasbora parva ...................................................... 19 1.2 Pseudorasbora parva eradication in the UK.................................................. 23 1.3 The Rosette Agent, Sphaerothecum destruens ............................................... 25 1.4 Life history traits of Sphaerothecum destruens .............................................. 29 1.5 Classification history of Sphaerothecum destruens ........................................ 32 1.6 Current Sphaerothecum destruens detection techniques ................................ 33 1.7 Environmental DNA as a detection tool ........................................................ 34 1.8 Mitochondrial DNA and its evolutionary trends ............................................ 36 1.9 Aims and objectives ...................................................................................... 40 1.10 Overview of the chapters ........................................................................... 41 Chapter 2 .................................................................................................................... 43 2.1 Introduction .................................................................................................. 44 2.2 Materials and methods .................................................................................. 45 2.2.1 18S ribosomal RNA (rRNA) .................................................................. 46 2.2.2 Internal transcribed spacer 1 (ITS 1) reaction conditions ........................ 47 2.2.3 Cytochrome b (Cyt-b) ............................................................................ 48 2.2.4 Determining specificity and sensitivity of the developed Sphaerothecum destruens-specific assays for ITS 1 and Cyt-b ..................................................... 49 2.2.5 Cross reactivity with other susceptible host fish species ......................... 50 2.2.6 Comparison of limit of detection in light of DNA extraction efficiency.. 50 2.3 Results .......................................................................................................... 53 2.3.1 Development of new detection methods for Sphaerothecum destruens ... 53 2.3.2 Detection limits of developed markers for S. destruens DNA in presence and absence of fish DNA P. parva ...................................................................... 54 2.3.3 Cross-reactivity with fish DNA .............................................................. 56 2 2.3.4 Limit of detection comparison ............................................................... 57 2.4 Discussion .................................................................................................... 58 2.5 Summary ...................................................................................................... 60 Chapter 3 .................................................................................................................... 61 3.1 Introduction ....................................................................................................... 62 3.2 Material and Methods ........................................................................................ 64 3.2.1 Fish Dissection ........................................................................................... 64 3.2.2 DNA Extraction.......................................................................................... 64 3.2.3 Sphaerothecum destruens detection using PCR ........................................... 64 3.2.4 Amplification of Pseudorasbora parva mitochondrial cytochrome b gene .. 65 3.2.5 Phylogenetic analysis ................................................................................. 65 3.2.6 Population demographic analysis ................................................................ 66 3.3 Results .............................................................................................................. 67 3.3.1 Sphaerothecum destruens detection and its prevalence across the sampled populations .........................................................................................................
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