Diversification patterns of Solanum L. (Solanaceae), plant macroecology and responses to land-use change a thesis submitted for the degree of Doctor of Philosophy in Life Science by Susy Echeverr´ıa-Londono˜ Department of Life Science Imperial College London London SW7 2BZ, United Kingdom 2018 Declaration of Originality I certify that this thesis, and the research to which it refers, are the product of my own work, unless mentioned here or in the text. I collected none of the ecological data. Data from Chapter 4 and 5 came from a number of researchers who have generously shared their data to the PREDICTS project. Chapter 5 has been published in the Journal “Diversity and Distributions” and has benefited from comments by co-authors and anonymous reviewers. Parts of the manuscript have been commented and proofread by my supervisors, Andy Purvis and Sandra Knapp, whereas others have been commented and proofread by the postdoctoral researchers Isabel Fenton and Adriana De Palma. Susy Echeverr´ıa-Londo˜no 2 Copyright Declaration The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work 3 4 Diversification patterns of Solanum L. (Solanaceae), plant macroecology and responses to land-use change Abstract Current patterns of biodiversity reflect, to a certain degree, the legacy effects of species adaptations to past environmental and geological settings. A more in-depth understand- ing of this history and the traits that shape it, therefore, will help us to improve our predictions of how species will respond to current environmental change. In this thesis, I apply different analytical approaches to a range of case studies at a variety of taxonomic and geographic scales to test the importance of this fundamental hypothesis. To examine the consequences of evolutionary and biogeographic history on the evolution of global biodiversity, in Chapter 2, I focus on the hyperdiverse plant genus Solanum (ca. 1300 species). This genus is an ideal case study since it combines a complete high-level phylogeny with global species distribution data, and covers an ecological spectrum from endemics to weeds. Chapter 2 shows that the vast diversity of Solanum is the result of at least two radiations. The majority of the lineages distributed in the Old World represent the most significant recent radiation, diversifying nearly twice as rapidly as any other group of solanums. This chapter also provides a brief comparison of the current approaches for modelling multi-rate diversification. In Chapter 3, I explore how the evolutionary legacy of colonisation, dispersal and climatic history have affected patterns of diversity in the genus. In this chapter, I show how successful colonisation of new areas and environmental changes can — but does not always — drive explosive diversification. In Chapter 3, I show how arid-adapted lineages within Solanum have benefited from widespread habitat drying over the last few million years. This successful expansion reveals the potential evolutionary capacity of this group to expand and colonise currently disturbed and open areas, which is supported by the spread of some species considered as weeds such as S. elaeagnifolium, S. torvum, S. nigrum. In Chapter 4, therefore, I undertake a global analysis to assess whether the climatic preferences that have shaped the macroevolution of Solanum are now also shaping plant macroecology worldwide. For this analysis, I broaden my taxonomic scope to consider all plants, analysing an extensive global database that I helped to compile on how terrestrial assemblages respond to land use change, using a simple and very coarse classification of land use. In this 5 chapter, I demonstrate that species adapted to mesic conditions are highly sensitive to habitat conversion, compared with widespread arid and warmer-adapted species. These results show how land-use and climate change may favour similar species, thus potentially increasing the rate of homogenisation caused in the Anthropocene. As shown in Chapter 4 species’ responses to current environmental changes vary widely, depending on their ecological traits and climatic adaptations. This heterogeneity of responses could drive significant rearrangements in the composition of ecosystems, es- pecially in the tropics where most of the species with narrow geographic and climatic ranges are found. In chapter 5, therefore, I quantify the impacts of land-use change on the composition of tropical assemblages using Colombia as a case study. In this chapter, I statistically analyse plant and animal data from 285 sites in Colombia to model how terrestrial assemblages are responding to land use change, using a much more finely- resolved land-use classification than that used in Chapter 4. I combine these models with four projections of land use to investigate how diversity is expected to change under future scenarios associated with different climate change policies. Here I demonstrate that land-use change has driven an increasing change in the composition of the ecological assemblages in Colombia and that depending on the policies implemented in the future, this negative effect could continue, risking the quality of ecosystems unless the impacts are mitigated. 6 To my husband, my aunt Vicky and my uncle Hermes. 7 Acknowledgments I would like to thank my PhD advisor, Professor Andy Purvis who gave me the oppor- tunity to join his team in Silwood Park as a master student and at the Natural History Museum as a PhD student. Thanks Andy for supporting me during the past five years and for helping me during this very challenging period of my life. I am also very grateful with my co-supervisor Dr Sandra Knapp for all her advice and trust during my PhD. Thanks Sandy for your enthusiasm and for sharing with me your knowledge and adven- tures. I also have to thank Tiina S¨arkinen and Natalie Cooper for their scientific advice and insightful discussions and suggestions. Natalie thanks a lot for all your help not only during my PhD but also in finding a Postdoc. I will forever be thankful to Isabel for all her advice, discussions, suggestions and proof- reading. Isabel your support was vital for me. I very much appreciate all the academic and personal conversations, which truly made a difference during my PhD. I also want to thank Adriana for all her statistical advice, proofreading and for all the hugs that she gave me when I most needed them. Thanks Adriana for all your good vibe and for buying me coffee and cake for my engagement and birthdays! I also want to thank my bachelor supervisor Daniel Rafael Miranda-Esquivel for all the training and advice. Everything I learned back in Colombia made a significant contribu- tion to my performance as a Masters and PhD student. I thank all the members of the Purvis lab: Katia, Rogier, Sara, Victoria, Dan, Sam, Helen, Adriana, Isabel and Connor for all the fun and for listening to my complaints every day (also for trying to understand what I was saying). We share a lot of fun moments but also some upsetting ones, 2016 and 2017, not the greatest years for the human race and the world in general. I also want to thank Dom who became an exceptional friend since the masters. Thanks Dom for all the movies, the coffee and our career crisis conversations. My latin girls! Katia, Belen, Blanca and Nadia. You made my time in the museum unforgettable. Thanks for all your support, the fun, the tears and all the coffee! I will miss you all! Belen, I will miss you so much. You became one of my best friends, and I 8 am grateful for all what you did for me during my time in London. I will never forget all the good and also the sad moments we share together. I would like to thank my aunt Vicky and uncle Hermes for all their support with my university studies. There is no doubt that without them I would never have achieved anything. There are no words to express how grateful I am for your trust, love and support. The best outcome for the last five years is finding my soul-mate and now husband, Francesco. Thank you for all your love, patience and support. Thanks for believing in me more than anyone else and helping me when sometimes I was sad and depressed. Thanks for choosing me as your life partner and for being as you are. I gratefully acknowledge the funding sources that made my PhD possible. I was par- tially funded by the Administrative Department of Science, Technology and Innovation of Colombia (COLCIENCIAS) for my masters and two years of my PhD. I also want to thank my husband and father-in-law for their financial support during the last two years of my PhD. 9 List of figures 1.1 Example of the floral morphology in Solanum species from different sub- clades or sections ............................... 25 2.1 Backbone tree of Solanum from S¨arkinen et al. (2015) ........... 35 2.2 Diversification shifts identified in the phylogeny of Solanum using MEDUSA 43 2.3 Overall mean net diversification rates of Solanum lineages obtained in BAMM 44 2.4 Average macroevolutionary cohort across the 100 trees obtained by PASTIS using the Solanum species in the S¨arkinen et al. (2013) phylogeny .... 45 3.1 Historical biogeographic events allowed in BioGeoBEARS ......... 59 3.2 Global distribution of the net diversification rates of Solanum.