Assessing human impacts on Lake Tanganyika cichlid fish communities Adam William Britton University College London A thesis submitted for the degree of Doctor of Philosophy February 2019 Declaration I, Adam William Britton, confirm the work presented in this thesis is my own. Where information has been derived from other sources, I confirm this has been indicated in the thesis. Adam William Britton Candidate 2 Statement of authorship I conducted field work in the Tanzanian section of Lake Tanganyika in 2015 to collect community composition data used in Chapters two and three, and to collect specimens used in Chapter four. Chris Doble collected extra specimens used in Chapter four in 2016 because my research permit was delayed whilst I was in Tanzania. Chapter two has been published in Biological Conservation with co- authors Julia Day, David Murrell, Chris Carbone, Kirsty Kemp, Chris Doble and Ben Ngatunga (Britton et al., 2017). I collected and analysed the data and wrote the first draft of the manuscript. Comments from Julia Day and David Murrell were incorporated into the text prior to publication. Reviewer’s comments regarding zeta diversity analysis in Chapter 2 supporting information Appendix S2.2 and S2.3, and Figure S2.3, S2.4 and S2.5 were carried out and added to the text by David Murrell. Morphological data in Chapter three was collected by myself at the British Natural History Museum and the Royal Museum of Central Africa in Belgium. Stable isotope analysis of samples from Chapter four was conducted at the Scottish Universities Environmental Research Centre (SUERC), Life Science Mass Spectrometry Facility in 2015 and 2016. I prepared and measured all samples and received training from Rona McGill (SUERC) to run sample on the mass spectrometer. Stomach content data was collected during the course of a Master’s research project that I oversaw (Calum Ramage, 2017). Chapter four is in press at Freshwater Biology, I wrote the first draft of the manuscript, and comments from Julia Day and David Murrell were incorporated into the text prior to submission. 3 Abstract This thesis assesses the human impacts on rocky shore cichlid fish communities from the biodiversity hotspot Lake Tanganyika, by comparing the diversity of its protected and unprotected areas. Chapters two and three use cichlid community composition data collected from a range of localities in the Tanzanian section of Lake Tanganyika, to investigate whether human impact is negatively affecting their species, functional, and phylogenetic diversity, and to assess whether protected areas are conserving these components of diversity. In terms of species diversity, alpha diversity was higher in protected areas than adjacent unprotected localities, and the pattern of beta and zeta diversity in protected areas indicate a more even community composition. Additionally, benthic feeding herbivores were the most affected trophic group. Functional diversity, which was defined as the shape variation of geometric morphometric landmarks reflecting key traits, was also higher in protected areas than adjacent unprotected localities, as was phylogenetic diversity. Furthermore, functional and phylogenetic diversity were both linked to species richness, possibly due to a lack of variation in species uniqueness. Chapter four investigates the possible reasons for changes in cichlid diversity in unprotected areas using stable isotope and stomach content analysis. Benthic feeding species from the most disturbed locality had significantly higher nitrogen stable isotopes and stomach sediment proportions than a less disturbed locality, which may contribute to the lower species diversity of this trophic group. In conclusion, protection from human disturbance prevents a reduction in the core components of cichlid fish diversity in Lake Tanganyika, and therefore the network of freshwater and terrestrial protected areas should be increased. Moreover, protection of species appears to be an effective conservation strategy for the core components of biodiversity, so species richness could be used as a surrogate for biodiversity assessments in other systems. 4 Impact Statement Assessing human impacts on fish communities in aquatic habitats is vital to ensure biodiversity is conserved and ecosystems are providing essential services such as a clean water source for all life. Conservationists have started to quantify different components of biodiversity to enable a more holistic protection of species and habitats. For instance, protecting functional diversity can improve the resilience of an ecosystem to change. Protected areas are a widely used strategy for conserving marine and terrestrial species, however, there are a lack of freshwater protected areas to conserve the numerous endangered freshwater species and habitats. Furthermore, the ability of protected areas to conserve morphological diversity and ecosystem functions is often not investigated. Cichlid fishes represent the most species rich group in biodiversity hotspot Lake Tanganyika, comprising 250 species, but like many freshwater systems, only a small proportion of Lake Tanganyika is formally protected. Despite this, there are few studies investigating how anthropogenic activities have impacted LT cichlid fish diversity, and whether they are conserved in the current protected area network. The research in this thesis provides a comprehensive diversity assessment of Lake Tanganyika cichlid fish communities, by investigating whether the current network of protected areas in Tanzania is conserving the core components of biodiversity. This thesis also provides a possible link to lower diversity encountered in human impacted sites. Academic outputs from this thesis include a peer-reviewed publication, with another under review. The publication is freely available online, and the data is on open access digital repository Dryad. Research has been presented at the British Ecological Society Annual Meeting and the Student Conference on Conservation Science. Samples collected will be vouchered at the British Natural History Museum for future use. The impact of the thesis also has policy implications. By demonstrating Tanzanian protected areas are conserving the core components of diversity this thesis provides recommendations for increasing Lake Tanganyika’s protected area network. The thesis also demonstrates that protecting species conserves other aspects of biodiversity, which can be used to inform conservation policy globally. 5 Acknowledgements First and foremost, thanks go to my supervisors at UCL Julia Day and David Murrell who have provided amazing support and guidance throughout my research project. Thanks to my co-supervisors Chris Carbone and Kirsty Kemp who always made me feel very welcome at the Zoological Society of London. Thanks to Chris Doble and Jane Hallam in the Day lab for their friendship along the way, and past members Antonia Ford and Claire Peart for all their help. Also, to Masters students Calum Ramage and Ana Da Silva. Thanks also to members of the Goswami lab for their help and friendship, Andrew Cuff, Thomas Halliday, Marcela Randau, Carla Bardua, Ryan Felice and Aki Watanabe. Several collaborators were instrumental to this research project. George Kazumbe from Kigoma in Tanzania for his help in the field. Ben Ngatunga from the Tanzania Fisheries Research Institute, for his help obtaining research permits from the Tanzania Commission for Science and Technology. Rona McGill at the Scottish Universities Environmental Research Centre (SUERC), Life Sciences Mass Spectrometry Facility was very helpful with training and guidance for stable isotope analysis. James Maclaine and Oliver Crimmen at the British Natural History Museum, and Emanuel Vreven at the Royal Museum of Central Africa for letting me photograph specimens. Funding is acknowledged from NERC for a case industrial studentship (NE/L009005/1), and a NERC grant in kind for use of the Life Sciences Mass Spectrometry Facility at East Kilbride. Also, a small research grant from the Fisheries Society of the British Isles. Lastly, thank you friends and family who have been so supportive over the last four years. Especially my parents, Esther, Ped, Dom, Mike, Liz, Dave, and most importantly Lilly, who has been so supportive of me every single day. 6 Table of Contents 1 Introduction ......................................................................................... 16 1.1 Biodiversity .................................................................................... 16 1.2 Freshwater ecosystems ................................................................ 21 1.3 Lake Tanganyika ........................................................................... 23 1.4 Cichlid fishes ................................................................................. 24 1.5 Threats to Lake Tanganyika rocky shore cichlid fishes ................. 28 1.6 Aims .............................................................................................. 31 2 Terrestrial-focused protected areas are effective for conservation of freshwater fish diversity in Lake Tanganyika .............................................. 32 2.1 Abstract ......................................................................................... 32 2.2 Introduction ................................................................................... 33 2.3 Materials and methods .................................................................. 37 2.3.1 Study localities .......................................................................