Allen, Laura (2019) The application of biodiversity indicators to infer ecosystem health in regenerating tropical forest. PhD thesis. https://theses.gla.ac.uk/40949/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] The application of biodiversity indicators to infer ecosystem health in regenerating tropical forest. Laura Allen Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences University of Glasgow January 2019 © Laura Allen 2019 1 1 Abstract 2 There are an overwhelming number of biodiversity indices and indicators 3 available for ecologists and conservationists to use when seeking to understand 4 how biodiversity responds to human disturbance. In choosing between measures 5 there is often an underlying assumption that if a measure works well for one 6 group it will be equally applicable to another. In this study, I use multiple taxa 7 to explore the performance of a wide range of alpha and beta diversity measures 8 for studying biodiversity responses to human disturbance in tropical forest. I 9 sampled 18 sites along a gradient of human disturbance from primary tropical 10 forest to banana monocultures in Peru. I chose three taxonomic groups and one 11 audio approach, which have all been suggested to be useful indicators for 12 studying biodiversity responses to disturbance: orchid bees (n = 1783), dung 13 beetles (n = 3787), butterflies (n = 2506) and soundscape samples (n = 6600). 14 This allowed me to identify how these groups responded to disturbance, which 15 diversity measures were most sensitive for detecting those changes and whether 16 the same measures were suitable for all groups. I used Hill numbers to measure 17 alpha diversity and explored beta diversity by looking at changes in community 18 composition and two new measures of beta diversity: redundancy and 19 representativeness. To see how the diversity patterns changed when taxonomic 20 similarity was considered, I used a recently developed family of similarity- 21 sensitive diversity measures and compared the results of these against more 22 traditional measures. I found that the diversity indices that were best for 23 detecting disturbance patterns varied widely among taxonomic groups. For dung 24 beetles, species richness and community composition were the most effective 25 measures, whereas these performed poorly for orchid bees. Abundance and 26 redundancy were more sensitive for detecting a response to disturbance in 27 orchid bees. Using the butterfly dataset, I show that the inclusion of species 28 similarity completely changed the diversity patterns found across the 29 disturbance gradient. The similarity of species present in a community is likely 30 to be important for the preservation of evolutionary adaptability and the 31 provision of ecosystem functions and I therefore suggest that diversity measures 32 based on similarity will be a useful additional tool for conservation and impact 33 assessments. Acoustic diversity showed unintuitive responses to disturbance, 34 with higher diversity detected in more disturbed forest, and more research is 2 35 required to assess the performance of different acoustic indices in rainforest 36 environments. Overall, my results demonstrate the importance of choosing 37 diversity indices carefully to suit the taxa being studied to avoid missing 38 important ecological responses, including a consideration of species similarity. I 39 recommend that, where possible, multiple diversity indices and taxonomic 40 groups should be used to reduce this risk and provide a comprehensive 41 understanding of ecosystem patterns in response to environmental change. 42 3 43 Table of Contents 44 Abstract ...................................................................................... 2 45 List of Figures ............................................................................... 7 46 List of Tables ................................................................................ 9 47 Acknowledgements ........................................................................ 10 48 Author’s declaration ...................................................................... 12 49 1 General Introduction ................................................................ 13 50 1.1 Tropical forests and their conservation ...................................... 13 51 1.2 Biodiversity monitoring ......................................................... 17 52 1.3 Biodiversity and ecosystem functions ........................................ 19 53 1.4 Indicators ......................................................................... 21 54 1.5 Quantifying biodiversity ........................................................ 24 55 1.6 Thesis aims and structure ...................................................... 28 56 2 Study area ............................................................................. 31 57 2.1 Introduction ...................................................................... 31 58 2.2 Data collection ................................................................... 35 59 2.3 Analysis ........................................................................... 38 60 2.4 Results ............................................................................ 39 61 2.5 Conclusion ........................................................................ 41 62 3 Dung beetles as indicators: what we measure matters. ....................... 43 63 3.1 Abstract ........................................................................... 43 64 3.2 Introduction ...................................................................... 44 65 3.3 Methods ........................................................................... 48 66 3.3.1 Study area ................................................................... 48 67 3.3.2 Data Collection ............................................................. 49 68 3.3.3 Analysis ....................................................................... 50 69 3.4 Results ............................................................................ 55 70 3.4.1 Alpha diversity .............................................................. 55 71 3.4.2 Functional groups ........................................................... 57 72 3.4.3 Beta diversity ............................................................... 57 73 3.4.4 Ecosystem functions ........................................................ 59 74 3.5 Discussion ......................................................................... 59 75 3.6 Conclusion ........................................................................ 64 76 4 Are orchid bees useful indicators of the impacts of human disturbance? ... 65 77 4.1 Abstract ........................................................................... 66 78 4.2 Introduction ...................................................................... 67 79 4.3 Materials and methods .......................................................... 70 80 4.3.1 Study area ................................................................... 70 4 81 4.3.2 Orchid bee diversity ........................................................ 72 82 4.3.3 Pollination services ......................................................... 77 83 4.4 Results ............................................................................ 78 84 4.4.1 Orchid bee diversity ........................................................ 78 85 4.4.2 Pollination services ......................................................... 84 86 4.5 Discussion ......................................................................... 85 87 4.6 Conclusion ........................................................................ 90 88 4.7 Data Access ....................................................................... 90 89 5 Exploring the use of similarity-sensitive diversity measures for detecting the 90 impacts of human disturbance: a case study on neotropical butterflies. ......... 91 91 5.1 Abstract ........................................................................... 91 92 5.2 Introduction ...................................................................... 91 93 5.3 Methods ........................................................................... 97 94 5.3.1 Study design ................................................................. 97 95 5.3.2 Data Collection ............................................................. 97 96 5.3.3 Analysis ....................................................................... 99 97 5.4 Results ........................................................................... 101 98 5.4.1 Alpha diversity ............................................................. 101 99 5.4.2 Beta diversity .............................................................. 105 100 5.4.3