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Assessing the Impacts of Environmental Change on British Pollinators (Syrphidae) Using Next Generation Sequencing Techniques

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Assessing the Impacts of Environmental Change on British Pollinators (Syrphidae) Using Next Generation Sequencing Techniques Assessing the impacts of environmental change on British pollinators (Syrphidae) using next generation sequencing techniques Hannah Norman Submitted for the degree of Doctorate of Philosophy Department of Life Sciences, Imperial College London Declaration of Originality All the work in this PhD is mine, and any programs, data and work which is not mine or was not carried out by me is referenced within the text. Copyright Declaration The copyright of this thesis rests with the author. Unless otherwise indicated, its contents are licensed under a Creative Commons Attribution-Non-Commercial 4.0 International License (CC BY-NC). Under this licence, you may copy and redistribute the material in any medium or format. You may also create and distribute modified versions of the work. This is on the condition that: you credit the author and do not use it, or any derivative works, for a commercial purpose. When reusing or sharing this work, ensure you make the licence terms clear to others by naming the licence and linking to the licence text. Where a work has been adapted, you should indicate that the work has been changed and describe those changes. Please seek permission from the copyright holder for uses of this work that are not included in this licence or permitted under UK Copyright Law. 1 Abstract British pollinating insects are vital for their contribution to crop yields as well as maintenance of semi-natural environments across the UK. The Syrphidae family are highly diverse and thought to be an important pollinating group. In order to understand the evolutionary relationships in this family, mitochondrial genomes were used to build the largest tree of the Syrphidae family to date. This tree was used to establish relative ages for divergences within the family, and to explore the evolution of diverse syrphid larval life histories. The recent introduction of a UK pollinator monitoring programme has resulted in a large amount of data with the potential to inform conservation and management, presenting an opportunity for DNA analysis. A CO1 reference database was curated and tested for UK syrphids, resulting in sequences for 70% of UK species and highlighting difficulties in DNA identification. Barcoding of syrphids was then expanded by also metabarcoding pollen from gut samples. This showed the diversity of plant – syrphid interactions at an individual level across three different land use types. It also highlighted the importance of including syrphid larval life histories in analyses of this family, as these appeared to have a larger effect on species composition than pollen composition did. Finally, the reach of this thesis was expanded to include non-bee and non-syrphid pan trap visitors from the pollinator monitoring programme. This highlighted the diversity of non- syrphid Dipterans and allowed species and phylogenetic diversity to be compared in these bulk insect samples. Using DNA methods to analyse monitoring data has the potential to increase our knowledge of cryptic species, phylogenetic diversity and pollinator associations. Alongside this, DNA can be used to analyse large datasets of diverse pollinating insects which otherwise would be overlooked. 2 Table of Contents Declaration of Originality .................................................................................................. 1 Copyright Declaration ....................................................................................................... 1 Abstract ............................................................................................................................ 2 List of table and figures ..................................................................................................... 5 Chapter 1 ................................................................................................................................... 5 Chapter 2 ................................................................................................................................... 5 Chapter 3 ................................................................................................................................... 5 Chapter 4 ................................................................................................................................... 5 Literature review ............................................................................................................... 6 Pollination .................................................................................................................................. 6 Syrphid pollinators ..................................................................................................................... 8 Monitoring ................................................................................................................................. 9 DNA monitoring ....................................................................................................................... 11 Plant – pollinator networks ...................................................................................................... 13 Phylogenetics ........................................................................................................................... 15 Conclusion ................................................................................................................................ 17 Chapter 1: Syrphidae Mitochondrial Genomes and Phylogeny ......................................... 18 Introduction ............................................................................................................................. 18 Methodology ............................................................................................................................ 21 Results ..................................................................................................................................... 25 Discussion ................................................................................................................................ 37 Conclusion ................................................................................................................................ 41 Chapter 2: Developing and testing a Syrphidae CO1 reference database ......................... 43 Introduction ............................................................................................................................. 43 Methodology ............................................................................................................................ 46 Results ..................................................................................................................................... 52 Discussion ................................................................................................................................ 63 Conclusion ................................................................................................................................ 67 Chapter 3: Hoverfly diversity and pollen associations in a semi-urban landscape ............. 68 Introduction ............................................................................................................................. 68 Methods ................................................................................................................................... 71 Results ..................................................................................................................................... 78 Discussion ................................................................................................................................ 95 3 Conclusion .............................................................................................................................. 100 Chapter 4: Metabarcoding of pan trap bycatch to identify non-bee and non-syrphid flower visitors .......................................................................................................................... 102 Introduction ........................................................................................................................... 102 Methods ................................................................................................................................. 104 Results ................................................................................................................................... 106 Discussion .............................................................................................................................. 117 Conclusion .............................................................................................................................. 122 Discussion ..................................................................................................................... 123 Acknowledgements ....................................................................................................... 127 Bibliography .................................................................................................................. 128 Supplementary Information .......................................................................................... 143 Chapter 1: Syrphidae Mitochondrial Genomes and Phylogeny ................................................ 143 Chapter 2: Developing and testing a Syrphidae CO1 reference database ................................. 145 4 List of table and figures Chapter 1 Table 1………………………………………………………………………………………………………………………….25
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