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A Thesis Submitted for the Degree of PhD at the University of Warwick Permanent WRAP URL: http://wrap.warwick.ac.uk/88401 Copyright and reuse: This thesis is made available online and is protected by original copyright. Please scroll down to view the document itself. Please refer to the repository record for this item for information to help you to cite it. Our policy information is available from the repository home page. For more information, please contact the WRAP Team at: [email protected] warwick.ac.uk/lib-publications Niche partitioning in Great British bats through dietary specialisation Roselyn Lydia Ware, BSc (Hons) Submitted for the degree of Doctor of Philosophy The University of Warwick School of Life Sciences July, 2016 Table of contents Table of contents ...................................................................................................................... i List of figures ........................................................................................................................ viii List of tables ............................................................................................................................ xi Acknowledgements .............................................................................................................. xiii Declarations ............................................................................................................................ xv Preface ................................................................................................................................... xvi List of common abbreviations ............................................................................................ xvii Chapter 1 : Introduction .......................................................................................................... 1 1.1. The global importance of bats and the threats they face ......................................... 1 1.2. Using diet to define the ecological niche ................................................................ 2 1.3. Factors that influence bat diets .............................................................................. 3 1.3.1. Feeding style .................................................................................................. 3 1.3.2. Predation using echolocation ......................................................................... 5 1.3.3. Dentition and feeding .................................................................................... 8 1.3.4. Emergence time and prey availability ............................................................ 9 1.3.5. Distributions and habitat selection of Great British bats ............................... 9 1.3.6. Migration ...................................................................................................... 10 1.4. Measuring the diets of bats.................................................................................. 10 1.4.1. Using environmental DNA sequencing......................................................... 11 1.4.2. Metagenomics .............................................................................................. 11 1.4.3. Applying faecal metagenomics to study mammalian diets ......................... 13 1.4.4. Technical considerations when working with DNA from guano .................. 14 1.5. Environmental context of the source material ...................................................... 15 1.6. The importance of reliable bat identification ........................................................ 16 1.6.1. The classification of bats .............................................................................. 17 1.6.2. Updating the traditional taxonomy .............................................................. 17 1.6.3. Great British bat taxonomy .......................................................................... 19 1.7. Scope and aims of thesis ...................................................................................... 23 1.7.1. Research hypotheses ................................................................................... 24 1.7.2 Outline of thesis ............................................................................................ 25 Chapter 2 : Great British bats form four dietary niches: a meta-analysis of bat diet data (1929-2016) ..................................................................................................................... 27 i 2.1. Abstract .............................................................................................................. 27 2.2 Introduction ......................................................................................................... 27 2.2.1. Rationale for measuring bat trophic ecology data ....................................... 28 2.2.2 Methodologies employed in measuring diet ................................................ 28 2.3. Methods.............................................................................................................. 30 2.3.1. Selection of studies ...................................................................................... 30 2.3.2. Analysis of data ............................................................................................ 31 2.4. Results ................................................................................................................ 32 2.4.1. Comparing the methods used to measure diet ........................................... 33 2.4.2. The diets of each bat species ....................................................................... 34 2.4.3. Dietary diversity and niche breadth ............................................................. 35 2.5. Discussion ........................................................................................................... 38 2.5.1. Methods used to measure bat diets ............................................................ 38 2.5.2. Guild structure and niche partitioning ......................................................... 38 2.5.3. Niche partitioning in cryptic sympatric species P. pipistrellus and P. pygmaeus ............................................................................................................... 39 2.5.4. Mechanisms of trophic partitioning ............................................................. 40 2.5.5. Trophic breadth and extinction risk ............................................................. 41 2.6. Conclusions ......................................................................................................... 41 Chapter 3 : Shotgun metagenomic analysis of guano DNA .............................................. 43 3.1. Abstract .............................................................................................................. 43 3.2. Introduction ........................................................................................................ 44 3.2.1. Selection of sequencing method .................................................................. 44 3.2.2. Avoiding biases ............................................................................................. 47 3.2.3. Pathogens carried by Great British bats ....................................................... 48 3.3. Materials and methods ........................................................................................ 50 3.3.1. Wet lab ......................................................................................................... 50 3.3.2. Bioinformatics .............................................................................................. 66 3.3.3. Statistical analyses ....................................................................................... 75 3.4. Results ................................................................................................................ 76 3.4.1. Hits before and after adapter removal and quality filtering ........................ 76 3.4.2. DNA fragmentation and damage ................................................................. 76 3.4.3. De-multiplexing sequence data.................................................................... 78 3.4.4. Metagenomic assignments .......................................................................... 80 ii 3.4.5. Rarefaction analysis ..................................................................................... 84 3.4.6. DNA sources ................................................................................................. 84 3.4.7. Dietary composition of guano .................................................................... 102 3.4.8. Variation in diet between bat species ........................................................ 103 3.4.9. Genome size adjustment............................................................................ 105 3.4.10. Dietary diversity, niche breadth, and overlap .......................................... 107 3.5. Discussion ......................................................................................................... 111 3.5.1. Guano quality ............................................................................................. 111 3.5.2. The impacts of hibernation on bat guano .................................................. 112 3.5.4. Dietary overlaps and feeding styles ........................................................... 117 3.5.5. Guild structure and niche partitioning of cryptic species .........................