Evaluation of the community response of ecological networks using complexity science by Xueke Lu Submitted for the degree of Doctor of Philosophy School of Electronic Engineering and Computer Science Queen Mary, University of London United Kingdom June 2016 Statement of originality I, Xueke Lu, 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 at the end of this thesis. 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 infor- mation derived from it may be published without the prior written consent of the author. Signature: Xueke Lu Date: 15/06/2016 i Abstract This thesis investigates network properties of natural food webs. In particular, it focuses on the effect that external disturbances have on their substructures and robustness. The importance of a network-level methodology lies in its capacity to capture entangling species interactions and identify inter-connecting properties in heterogeneous food webs. The research first analysed the responses of freshwater food webs under the stress of drought. A core/periphery structure was detected and its relative size was found to be unchanged after drought despite a significant biodiversity loss. Species extinction trig- gered extensive link rewiring and movement of species from the core to the periphery. These results showed that the robustness was maintained indicating that the redundancy in the core can effectively mitigate species level perturbations. Secondly, the research further examined the effects of Genetically Modified Herbicide Tolerant (GMHT) man- agement on food web properties and robustness. Network analysis showed that such change in farming practice has no significant impact on the agro-ecosystems. However, crop switching, a common practice in agriculture, was found to pose much more signif- icant changes on network properties and robustness when compared to GMHT crops. Thirdly, the research examined over 50 empirical food webs and demonstrated that the relative core size is a much more effective indicator of food web robustness than the clas- sical ecological measure connectance, as the latter was found to be insensitive to changes in the interaction patterns. Lastly, the research established the relationships between centrality measures and species ecological and/or functional role in food webs, and how they impact on network robustness. ii TO MY FAMILY Acknowledgments First of all, I thank Athen Ma and Steve Uhlig who gave me an offer of this PhD position. During which I have been given invaluable guidance from my main supervisor Athen, who have taught me how to conduct research and write academic papers and manage multiple tasks and handle problems. I also thank my co-supervisors Steve, Guy Woodward and Ra´ulMondrag´on,who always support me and and provide pertinent guidance on research whenever I need them. I thank Chinese Scholarship Council (CSC) and Queen Mary who have funded my PhD. Additionally, I was given the opportunities to collaborate with Mark E ledger, David A Bohan, and other brilliant people. I also learned quite a lot through meetings and discussions with Eoin O'Gorman, Lei Zhao, and Samuel Johnson. Those experiences were not always available for a PhD student, and I really appreciate it. Finally, I would like to thank my colleague Clare Gray, who has helped me countless times on my English writing and my Thesis. I also thank Weisi Guo, Haroon Mumtaz, Hamed Haddadi, Sam, Ra´ul,and Steve, who helped me with my thesis and the proofreading. In addition, I thank my friends Shenglan Huang, Anqi He, Dantong Liu, Xiang Xu, Xinyue Wang, Hanbing Mu, Yunong Pang, Fei Dong, Liran Sun, Yanxu Meng, and Momo Zheng, who have helped me in many ways, and looked after me whenever I need them. Last but not least, I thank my parents in China, who have unconditionally supported me during the past four years. iv Table of Contents Abstract ii Acknowledgments iv Table of Contents v List of Figures x List of Tables xxi 1 Introduction 1 1.1 Food webs . .1 1.1.1 The emergence of a network approach . .1 1.1.2 Existing network analysis on food webs . .2 1.1.3 Network analysis on substructures . .4 1.2 Food web robustness . .5 1.3 Node centrality metrics . .7 1.4 Research novelty . .8 1.5 Thesis organisation . .8 2 Data and Methods 10 2.1 Data . 11 2.2 Food web analysis metrics . 13 2.3 Substructures . 14 v 2.3.1 Rich-core profiling . 16 2.3.2 The rich-club coefficient . 18 2.3.3 Food web redundancy . 19 2.4 Food web robustness measurement . 20 2.5 Statistical evaluation methodology . 23 2.5.1 Correlation (Pearson and Spearman) . 23 2.5.2 Null model . 24 2.5.3 Z-score . 25 2.5.4 Bray-Curtis dissimilarity . 25 2.6 Spanning tree . 26 2.7 Centrality indices . 27 3 Effect of drought on food web substructures 33 3.1 Research background and overview . 33 3.2 Methods . 34 3.2.1 Data set . 34 3.2.2 Core/periphery profiling and the rich-club coefficient . 35 3.2.3 Null model comparison . 36 3.2.4 Statistical tests . 36 3.2.5 Food web robustness . 37 3.3 The impact of drought on food web substructures . 38 3.3.1 Cores in food webs . 38 3.3.2 Species Extinction under drought . 42 3.3.3 Species Movement under drought . 45 3.3.4 Link density within the core . 50 3.3.5 Food web robustness . 52 3.4 Summary . 54 4 Network analysis on agroecosystems 56 4.1 Research background and overview . 56 vi 4.2 Methods . 57 4.2.1 Data set . 57 4.2.2 Individual and aggregated food web construction and analysis . 58 4.2.3 Substructure analysis . 59 4.2.4 Food web robustness . 60 4.2.5 Statistical analysis on network properties . 60 4.3 Impact of agricultural practice on species level properties . 61 4.4 Impact of agricultural practice on food web network properties . 63 4.4.1 Food web properties . 63 4.4.2 The core and its link density . 65 4.4.3 Substructure species composition and turnover . 69 4.4.4 Recurrent core substructures . 72 4.5 Impact of agricultural practices on food web robustness . 74 4.6 Summary . 75 5 Core redundancy governs food web robustness 77 5.1 Research background and overview . 77 5.2 Methods . 78 5.2.1 Data set . 78 5.2.2 Constructing a spanning tree . 79 5.2.3 Quantifying core and periphery redundancy . 81 5.2.4 Food web robustness . 83 5.3 Redundancy in substructures . 83 5.3.1 Spanning tree in empirical food webs . 83 5.3.2 Stream food webs under different pH levels . 87 5.4 The importance of core substructure to robustness . 88 5.4.1 Correlation between core size and robustness . 88 5.4.2 Robustness under random removal . 90 5.4.3 Substructure removal . 91 vii 5.5 Summary . 93 6 Centrality and food web robustness 95 6.1 Research background and overview . 95 6.2 Methods . 97 6.2.1 Cumulative node centrality . 97 6.2.2 Comparing robustness under different node removal sequences . 98 6.3 Network properties and centralities for food webs . 98 6.3.1 Distribution of node centrality metrics . 99 6.3.2 Implications of different centrality metrics to food webs . 101 6.4 Robustness - removal sequences . 105 6.4.1 Comparison between targeted removal and random removal . 106 6.4.2 Secondary extinction gradient through species removal . 106 6.5 Correlation between centralities and network properties . 109 6.6 Summary . 110 7 Conclusions and Future work 112 7.1 Conclusions . 112 7.2 Future work . 115 Appendix A Author's publications 119 Appendix B Supplementary data and results 121 B.1 Z-score evaluation on the rich-club coefficient with random networks . 121 B.2 Core/periphery examples . 123 Appendix C Food web data 125 C.1 53 standard food web data . 125 C.2 Food web robustness under different centrality rankings . 130 C.3 Species centrality in colour gradient . 138 C.4 Correlation analysis among node centrality rankings . 146 viii References . 151 ix List of Figures 1.1 Three freshwater food webs (a - Old Lodge, b - Afon Gwy, c - Broad- stone) plotted in trophic levels. Black nodes are detritus, green nodes are producers, and the rest are higher level predators. Predators, especially those from the second trophic level, share similar connectivity patterns with their prey. .4 2.1 An example of a simple food web containing two resource species (labelled as R) and two consumer species (labelled as C) that feed upon the two resource species. Both the energy transfer direction and trophic level are labelled. 12 2.2 A typical example of a core (formed by red nodes)/periphery (formed by the rest of black nodes) structure. Red nodes also formed the rich-club in the network. 15 2.3 a - Synthetic food web under control condition.