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INTROGRESSION PATTERNS in SCOTTISH BLUE MUSSEL (Mytilus Edulis) POPULATIONS

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INTROGRESSION PATTERNS in SCOTTISH BLUE MUSSEL (Mytilus Edulis) POPULATIONS INTROGRESSION PATTERNS IN SCOTTISH BLUE MUSSEL (Mytilus edulis) POPULATIONS Joanna Wilson Thesis submitted for the degree of Doctor of Philosophy Faculty of Natural Sciences Institute of Aquaculture 30th September 2016 Abstract Background: The blue mussel, Mytilus edulis L., is an important contributor to the shellfish sector of Scottish aquaculture, with 7,270 tonnes worth £8.8 million being produced for the year 2015. Since 2010, production values have fluctuated as a result of inconsistent spat settlement, several business closures, and heightened levels of marine toxins in some areas. On Scotland’s west coast, some farms (most notably Loch Etive) have suffered production losses from the appearance of non-marketable mussels with particularly fragile shells and poor quality meat. Recent research has demonstrated that these undesirable traits have a genetic factor, linked to the presence of a non-native but related species Mytilus trossulus (Gould, 1850) and often its hybrids with the native M. edulis. M. trossulus has been classed as a commercially damaging species under Scottish law, but there is insufficient data on hybridisation and introgression patterns in Scottish mussel populations to evaluate any possible impacts this could have on production. Existing research has focused on single locus genotyping to identify Mytilus spp. and their hybrids in Scotland. By instead utilising multilocus genotyping, introgression could be identified and a better understanding of population structure could be gained, with implications for management to maintain productivity and profitability. The aim of the research presented here was to develop and validate a suite of new species diagnostic markers for multilocus genotyping of field populations of Scottish mussels, thereby establishing a more complete picture of the taxonomic relationships between species than previous studies have permitted. Results: Analysis of SNPs identified with RADseq confirmed the presence of three genetically distinct Mytilus species in Scotland: M. edulis, M. galloprovincialis and M. trossulus. RADseq and KASP genotyping technology successfully identified and validated a suite of 12 highly robust diagnostic SNP markers for multilocus genotyping of Mytilus mussel populations. These markers permitted more comprehensive genotyping than previous studies had, allowing presumed pure species individuals to be distinguished from first generation (F1) hybrids and introgressed (FX) genotypes in reference populations, and subsequently presented the possibility of exploring introgression in a wider scale study. Multilocus genotyping of mussel populations from around Scotland revealed widespread introgression of M. edulis with both M. galloprovincialis and M. trossulus. No pure M. galloprovincialis was identified and pure M. trossulus was restricted to a single site in Loch Etive, possibly part of a relict population. F1 hybrids between M. edulis and M. trossulus were identified in Loch Etive and in Loch Fyne on the west coast. This was evidence of ongoing hybridisation and suggested an active hybrid zone existed in Scotland, something that previous single locus genotyping studies had not acknowledged. A link between shell fragility and M. trossulus introgression was recognised at a single site outside of Loch Etive, but this was not apparent anywhere else and the actual causes of shell fragility remain unevaluated. There was a clear difference between the genetics of most farmed stock and wild populations, which indicated an anthropogenic effect on introgression and subsequent species composition, and had implications for future farm site selection and broodstock sourcing. Temporal species composition in Loch Etive differed over a short time period, but high proportions of M. trossulus alleles were observable some 25 months after a major fallowing event had taken place. Pure M. trossulus was also identifiable, which was consistent with the presence of an established population of M. trossulus existing in this area. Conclusion: Multilocus genotyping has produced a more in depth picture of species diversity in Scottish mussel populations. SNP assays revealed widespread introgression between three genetically distinct species – M. edulis, M. galloprovincialis and M. trossulus – and furthermore recognised that, to date, single locus genotyping has overestimated the abundance of pure Mytilus mussels in Scottish waters. However, this hitherto unidentified genetic complexity does not appear disadvantageous to mussel production, despite the prevalence of M. trossulus introgression among farmed populations, and it is somewhat unlikely that genetics are the sole cause of undesirable shell characteristics among Mytilus spp. mussels. Declaration I, Joanna Wilson, hereby certify that this thesis is a unique piece of work that has been composed entirely by myself; which embodies the results of my own research; and which has not been submitted for any other higher degree or qualification. All sources of information have been suitably acknowledged in the text. Acknowledgements A special thanks to my parents and sisters, and to all of my friends (old and new; Cricetid and Canid pets included) for their invaluable support during my PhD. I am grateful for your patience and perseverance with this emotional wreck during what has felt like a tremendously long slog: I do not take it for granted how important you have been in helping me stay focused and motivated, and however clichéd it sounds I know that I could not have done this without you! Thanks to my supervisors for their guidance and encouragement throughout the study, and thanks to MASTS and Marine Scotland Science for their financial support. Additional thanks to all farmers and researchers who provided me with specimens: your insights into the shellfish industry and the associated science have been most illuminating to someone who, before starting this PhD, knew absolutely nothing about mussels and had only worked with small, furry mice. The list of other people who have helped me out in one way or another, and the list of things that they have helped me with, would fill another thesis in itself. To save myself that pain, I shall instead conclude by simply thanking everyone else who has helped me with even the most mundane of tasks during my PhD, and let you know that I have appreciated your assistance in whatever form it took. Table of Contents List of Figures ........................................................................................................... i List of Tables .......................................................................................................... iv List of Equations ..................................................................................................... vi Abbreviations and Acronyms ................................................................................ vii CHAPTER 1 – GENERAL INTRODUCTION 1.1. BACKGROUND .............................................................................................. 1 1.1.1. Shellfish aquaculture in Scotland .................................................................. 1 1.1.2. Mytilus spp. life history ................................................................................. 4 1.2. HYBRIDISATION AND INTROGRESSION ................................................. 7 1.2.1. Hybrid zones .................................................................................................. 8 1.2.2. Barriers to hybridisation and introgression .................................................. 10 1.3. GENOTYPING FOR SPECIES IDENTIFICATION .................................... 11 1.3.1. Genotyping the Mytilus edulis species complex .......................................... 12 1.3.1.1. Allozymes ................................................................................................. 12 1.3.1.2. Single locus DNA-based markers ............................................................. 13 1.3.1.3. Microsatellites and SNPs .......................................................................... 14 1.3.1.4. Mitochondrial DNA markers .................................................................... 15 1.3.2. Multilocus genotyping ................................................................................. 16 1.4. DNA SEQUENCING AND GENOTYPING ................................................. 17 1.5. METHODS FOR POPULATION GENETIC ANALYSIS ........................... 19 1.6. THESIS AIMS AND OBJECTIVES .............................................................. 20 CHAPTER 2 – GENERAL MATERIALS AND METHODS 2.1. SAMPLE COLLECTION ............................................................................... 22 2.2. DNA EXTRACTION, QUALITY ASSESSMENT AND CLEANUP .......... 25 2.2.1. Automated DNA extraction ......................................................................... 25 2.2.2. Manual DNA extraction ............................................................................... 26 2.2.2.1. SSTNE/SDS DNA extraction ................................................................... 27 2.2.2.2. RealPure DNA extraction ......................................................................... 28 2.2.3. DNA quantification and quality assessment ................................................ 28 2.2.3.1. Spectrophotometry .................................................................................... 28 2.2.3.2. Gel electrophoresis ..................................................................................
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