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Towards a Networks Based Approach to Biomonitoring

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Towards a Networks Based Approach to Biomonitoring Towards a networks based approach to biomonitoring Clare Gray School of Biological and Chemical Sciences Queen Mary University of London A thesis submitted to the University of London for the degree of Doctor of Philosophy February 2016 Statement of originality I, Clare Gray, confirm that the research included within this thesis is my own work or that where it has been carried out in collaboration with, or supported by others, that this is duly acknowledged below and my contribution indicated. Previously published material is also acknowledged below. I attest that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge break any UK law, infringe any third party’s copyright or other Intellectual Property Right, or contain any confidential material. I accept that the College has the right to use plagiarism detection software to check the electronic version of the thesis. I confirm that this thesis has not been previously submitted for the award of a degree by this or any other university. The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without the prior written consent of the author. Signature: Date: 12/2/16 Page | i Details of collaboration and publications: Chapter one: This text is adapted from work was done alongside many co-authors, which was published in Journal of Applied Ecology in 2014. Myself and Guy Woodward conceived the original idea, I organised a meeting and invited co-authors, I then organised contributions from co-authors and edited them into the final document. All co-authors contributed towards the final text. The full list of co-authors is: Clare Gray, Donald J. Baird, Simone Baumgartner, Ute Jacob, Gareth B. Jenkins, Eoin J. O’Gorman, Xueke Lu, Athen Ma, Michael J. O. Pocock, Nele Schuwirth, Murray Thompson and Guy Woodward. Full permission to reproduce the text and figures here has been received. See here for the online version: http://onlinelibrary.wiley.com/doi/10.1111/1365- 2664.12300/abstract Chapter two: This chapter was published in Food Webs in 2015, and appears here with appropriate permissions from the publisher. I conceived the original idea alongside Guy Woodward. Myself, Dan Perkins and Lawrence Hudson then developed these ideas further and designed the analysis. Lawrence Hudson wrote the R code for the function itself. I did all the analysis and wrote the manuscript. All co- authors contributed towards the final text. The full list of co-authors is: Clare Gray, David H. Figueroa, Lawrence N. Hudson, Athen Ma, Dan Perkins and Guy Woodward. Full permission to reproduce the text and figures here has been received. See here for the online version: http://www.sciencedirect.com/science/article/pii/S2352249615300045 Chapter 3: This work was done with data belonging to the Upland Waters Monitoring Network. I conceived the original idea alongside Guy Woodward and Athen Ma. I developed it, conducted the analysis and wrote the manuscript. It is planned that this chapter will be submitted to Advances in Ecological Research in early 2016. The full list of co-authors is: Clare Gray, David McElroy, Xueke Lu, Athen Ma, Don Monteith, Page | ii Ewan Shilland and Guy Woodward. Chapter 4: This work was done alongside David Bohan, Órla McLaughin and Sandrine Petit from Institut National de la Recherche Agronomique in Dijon, France. I conceived the original idea, alongside David Bohan and Órla McLaughlin, we then developed that idea and the analysis. I conducted the analysis and wrote the manuscript with input from David Bohan. All co-authors contributed towards the final text. It is planned that this chapter will be submitted to Current Biology in early 2016. The full list of co-authors is: Clare Gray, Athen Ma, Órla McLaughin, Sandrine Petit, Guy Woodward, David Bohan. Chapter 5: This was a large project involving many organisations. Guy Woodward and Murray Thompson conceived the original sampling design. I led the fieldwork and much of the lab work for the food web analysis, whilst supporting Murray Thompson with the remaining fieldwork. He and I processed and identified the invertebrates from September 2013 and March 2014, I supervised students (Laura Palmer, Amy West, Marie-Clare Danner and Masamichi Fujisawa) who processed the invertebrates from September 2014 and March 2015. Carl Sayer, Laura Rutland and Scot Warren processed and identified the diatom samples from September 2013, March 2014 and September 2014. Murray Thompson processed the leaf litter bags from September 2013 and March 2014, I then supervised Amy West who processed the bags from September 2014 and March 2015. I supervised students Laura Palmer and Cara Patel to process the Chlorophyll samples. I constructed the food webs and did all the analysis presented here. The data from September 2013 was published by Freshwater Biology in 2015 (Appendix C). I contributed the food web analysis and text directly to the manuscript (Appendix C) although I was not the lead author. Appendix A: This work has been done alongside collaborators Samraat Pawar and Katharina Brink from Imperial College London, Ian Donohue from Trinity College Dublin and Xueke Lu, Athen Ma and Guy Woodward. I conceived and developed the original idea with conversations with each of the collaborators. Katharina Brink Page | iii provided R code to measure the Mutual Information of the food webs. Appendix B: This manuscript has been submitted to Nature Climate Change, at the time of writing we are responding to a second round of reviewers’ comments. I have worked alongside Xueke Lu and Athen Ma since the beginning of this project, I am joint first author with Xueke Lu. Athen Ma, Xueke Lu and I have met regularly to discuss the analysis and writing up of this project, Xueke Lu has done all the analysis and I wrote the initial manuscript draft. All co-authors contributed to the final submitted draft. The full list of co-authors is: Xueke Lu, Clare Gray, Lee Brown, Mark Ledger, Alexander Milner, Raúl Mondragón, Guy Woodward and Athen Ma. Appendix D: This work was published as a chapter in the book ‘Aquatic Functional Biodiversity: Ecological and Evolutionary Approaches’ and was done alongside co- authors. I organised a meeting and invited co-authors, I then organised contributions from co-authors and edited them into the final document. All co-authors contributed towards the final text. The full list of co-authors is: Clare Gray, Iliana Bista, Simon Creer, Benoit Demars, Francesco Falciani, Don Monteith, Xiaoliang Sun and Guy Woodward. Full permission to reproduce the text and figures here has been received. Page | iv Abstract Effective monitoring of the environment for anthropogenic impacts is essential for managing and conserving ecosystems, especially in the face of global climate change and an ever increasing human population. Yet current biomonitoring schemes are grounded in species or trait based approaches, and lack the tools required to deal with the effects of stressors on species and their interactions in complex natural systems. Ecological networks can offer new insights into ecosystem degradation by explicitly considering the interactions between species, adding value to current taxonomically constrained schemes. Here, I develop a formalisation of a method for constructing ecological networks from species lists and trophic information harvested from the primary literature (Chapter 2). I then use this method to augment traditional biomonitoring data with information on the interaction between species to build large collections of food webs (Chapters 3-5). I apply novel network analysis methods from complex network research to examine the substructure of these networks. In Chapter 3, I find that the structure, and substructure, of freshwater food webs are fundamentally altered by hydrochemical stress (Appendix A). Chapter 4 demonstrates that the structure of agricultural food webs are linked to the delivery of beneficial pest control services, potentially allowing those services to be enhanced through management of food web structure. Finally, in Chapter 5 I use more detailed food web data to investigate how freshwater food webs are impacted by a catastrophic pesticide spill, how the indirect effects propagate through the food web, and how the structure of the community and ecosystem functioning recover over time. The findings presented herein demonstrate that ecological networks constructed from routine biomonitoring data can be a useful tool for understanding the impacts of stressors on ecological communities. Considering the interactions between species is vital if we are to fully understand, and mitigate against the negative effects of global climate change on biodiversity. Page | v Acknowledgements Firstly, I’d like to thank my supervisors, Dr Athen Ma and Professor Guy Woodward for initially giving me the opportunity to take on this project, and then supporting and guiding me through it. Additionally, they have given me many opportunities to get involved in some fantastic side projects which have really allowed me to get as much out of my time as a PhD student as I could. Mark Trimmer acted as my panel chair throughout my PhD, as well as took over as surrogate supervisor when I needed it, and he always provided me with useful feedback and interesting analysis ideas during our panel meetings. The Woodward lab group (both past and present) have been unfailingly supportive and helpful, Dan Perkins, Eoin O’Gorman, Órla McLaughlin, Murray Thompson and Becca Kordas were always there to talk through ideas and problems with me. Xueke Lu has patiently answered my silly questions without fail. So many, many people have helped with the Kennet project and made the rigorous fieldwork schedule possible, in particular Marie-Claire Danner, Joseph Huddart, Manon Czuckermand, Laura Palmer, Laura Rutland, Amy West, Masamichi Fujisawa and Cara Patel. Thanks also to the many people I have bothered for help under the guise of a collaboration; David Bohan, Ewan Shilland, Don Monteith, Lawrence Hudson, Samraat Pawar, Ian Donohue and Katharina Brink.
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