House dust mites and their genetic systems Thesis submitted for the degree of Doctor of Philosophy School of Biological Sciences Kirsten M. Farncombe July 2018 Declaration Declaration: I confirm that this is my own work and the use of all material from other sources has been properly and fully acknowledged Kirsten M. Farncombe 1 Table of Contents Declaration................................................................................................................................ 1 Abstract ..................................................................................................................................... 8 Acknowledgements .................................................................................................................. 9 Chapter 1: Knowledge and Applications of House Dust Mites ......................................... 11 1.1 Ecology of House Dust Mites .................................................................................. 12 1.1.1 Mites in the home: ............................................................................................. 12 1.1.2 Life cycle: .......................................................................................................... 12 1.1.3 Humans in the home: ......................................................................................... 13 1.1.4 Pets in the home: ................................................................................................ 13 1.1.5 Colonisation of mites: ........................................................................................ 14 1.2 Taxonomy of Mites .................................................................................................. 16 1.2.1 Accuracy: ........................................................................................................... 16 1.2.2 The Acariformes: ............................................................................................... 16 1.2.3 The Parasitiformes: ............................................................................................ 18 1.2.4 Published mite genomes: ................................................................................... 20 1.3 Relevance of Mites ................................................................................................... 23 1.3.1 Medical importance: .......................................................................................... 23 1.3.2 Economic importance: ....................................................................................... 24 1.3.3 Forensic importance: .......................................................................................... 25 1.4 Various Genetic Systems in Mites.......................................................................... 26 1.4.1 Diploidy: ............................................................................................................ 26 1.4.2 Thelytoky: .......................................................................................................... 26 1.4.3 Arrhenotoky: ...................................................................................................... 27 1.4.4 Pseudo-arrhenotoky: .......................................................................................... 28 1.5 Population Genetic Structure in Mites: ................................................................ 30 1.5.1 Fragmented habitats: .......................................................................................... 30 1.5.2 Tetraynchus urticae population structure: ......................................................... 31 Chapter 2: Compiling a Database of House Dust Mites and Geographic Location ........ 32 2.1 Introduction ............................................................................................................. 32 2.2 Materials and Methods ........................................................................................... 33 2.2.1 Collection of published research:....................................................................... 33 2.2.2 Publication parameters: ...................................................................................... 34 2 2.3 Results and Discussion ............................................................................................ 35 2.3.1 Database from the literature: .............................................................................. 35 2.3.2 Assessing completeness of the database: ........................................................... 38 2.3.3 Limitations of the dataset and how they have been mitigated: .......................... 46 a. Number of studies: .......................................................................................................................... 46 b. External variants: ............................................................................................................................ 47 c. Collection methods: ........................................................................................................................ 47 d. Publication bias: .............................................................................................................................. 48 2.3.4 Applications of the database: ............................................................................. 49 2.4 Conclusions .............................................................................................................. 54 Chapter 3: Biogeographical Distribution of House Dust Mites ......................................... 56 3.1 Introduction ............................................................................................................. 56 3.2 Materials and Methods ........................................................................................... 57 3.3 Results and Discussion ............................................................................................ 58 3.3.1 Distribution by biogeographical region: ............................................................ 58 3.3.2 Distribution by country: ..................................................................................... 58 3.3.3 Latitudinal diversity gradient: ............................................................................ 60 3.3.4 Pleistocene glaciation: ....................................................................................... 61 a. Hypothesis: ..................................................................................................................................... 61 b. Select species supporting this hypothesis: ...................................................................................... 63 c. Issues with this hypothesis: ............................................................................................................. 63 3.3.5 Niche conservatism: ........................................................................................... 64 a. Hypothesis: ..................................................................................................................................... 64 b. Select species supporting this hypothesis: ...................................................................................... 65 c. Issues with this hypothesis: ............................................................................................................. 66 3.3.6 Tropical conservatism hypothesis: ..................................................................... 66 a. Hypothesis: ..................................................................................................................................... 66 b. Select species supporting this hypothesis: ...................................................................................... 68 c. Issues with this hypothesis: ............................................................................................................. 69 3.3.7 Time and area hypothesis (Time-for-speciation effect): .................................... 71 a. Hypothesis: ..................................................................................................................................... 71 b. Select species supporting this hypothesis: ...................................................................................... 72 c. Issues with this hypothesis: ............................................................................................................. 73 3.3.8 Species-energy hypothesis: ................................................................................ 73 a. Hypothesis: ..................................................................................................................................... 73 b. Select species supporting this hypothesis: ...................................................................................... 75 c. Issues with this hypothesis: ............................................................................................................. 76 3 3.3.9 House dust mites and the latitudinal diversity gradient: .................................... 77 a. Most likely hypotheses: .................................................................................................................. 77 b. House dust mites and the latitudinal diversity gradient: ................................................................. 78 3.4 Conclusions .............................................................................................................. 83 Chapter