Is speciation faster in the Tropics? Comparison of diversification rates between temperate and tropical Berberis L. (Berberidaceae) Nicolás Lavandero López 19/08/2016 Thesis submitted in partial fulfillment for the MSc in the Biodiversity and Taxonomy of Plants 1 ABSTRACT The Latitudinal Diversity Gradient (LDG) is one of the most common observed and studied patterns in ecology. The study of the uneven distribution of species across the globe has nourished a body of ecologic theories, with several hypotheses proposed in order to explain this pattern. LDG has been suggested to be caused by higher speciation rates in the tropics compared with temperate regions. In order to test this hypothesis, a phylogeny of the mostly Northern Temperate but also South American genus Berberis was constructed and dated. Nuclear ITS and chloroplast ndhF regions were used to build a molecular phylogeny representing most of the sections of Berberis found in the Northern Hemisphere and South America. Bayesian diversification analyses were done using the time-calibrated phylogeny. Our results suggest a significant rate shift in diversification near the base of Berberis, with no further increase in speciation rates towards the tropics. The evidence suggests no significant differences in speciation for Berberis between tropical and temperate zones. Further studies will be required to test whether higher rates detected in the Himalayan clade are linked to the mountain uplift. 2 ACKNOWLEDGEMENTS First, I would like to thank to my great supervisors, James Richardson, Tiina Sarkinen and Bhaskar Adhikari. Without your help, suggestions, last minute corrections and their valuable support I would not have survived at the last three months. Collecting samples and fieldwork is an exhausting task. I would like to thank Carlos and Andres for their collections in Colombia, the Jardin Botanico de Bogota Jose Celestino Mutis for the material provided. To Jim Solomon of the Missouri Botanical Garden, Federico Luebert, and Joao Stehmann for kindly providing samples from South America. I wish to thank Laura Forrest and Michelle Hart for the training, the constant help in solving all my issues during lab work. The last year would not have been the same without all my fellow MSc buddies. Thanks for making this year a memorable time. In particular, to Marita for bringing happiness and laughs, to Camila for sharing her Patagonian warmth and to Ludovica for helping me doing the acknowledgements and for saving me from eating instant couscous the all year. To my adoptive parents Ricardo, Lucia and Gin for hosting me in the very first days of this experience abroad. Last but not least, I wish to thank my family for encouraging me to come to Edinburgh and for their understanding throughout all these years of University. 3 Table of Contents Abstract ................................................................................................................................. 1 Acknowledgements ............................................................................................................... 2 List of Figures ....................................................................................................................... 5 List of Tables ......................................................................................................................... 6 1. Introduction ....................................................................................................................... 7 1.1 Patterns of biodiversity: the latitudinal gradient .......................................................... 7 1.1.1 Ecological Hypotheses .................................................................................... 8 1.1.2 Historical and Evolutionary hypotheses ............................................................... 9 1.2 Diversity in the Neotropics and Andean Orogeny ..................................................... 11 1.3 Himalayan uplift and Biodiversity ............................................................................ 13 1.4 Divergence time estimations using molecular and fossil data ................................... 13 1.5 Inference of differential rates of species diversification ........................................... 16 1.6 Introduction to Berberis............................................................................................. 16 1.7 Study Aims ................................................................................................................ 18 2. Materials and Methods .................................................................................................... 19 2.1 Taxon sampling ......................................................................................................... 19 2.2 Laboratory Methods .................................................................................................. 20 2.3 Sequence Alignment .................................................................................................. 22 2.4 Phylogenetic analysis ................................................................................................ 22 2.5 Fossil Calibration ....................................................................................................... 24 2.6 Divergence Age Estimation ....................................................................................... 24 2.7 Calculation of diversification rates using BAMM software ...................................... 26 3. Results ............................................................................................................................. 28 3.1 Phylogenetic analysis ................................................................................................ 28 3.2 Divergence time estimation ....................................................................................... 30 3.3 Rate Shifts And Diversification rates ........................................................................ 32 4. Discussion ....................................................................................................................... 40 4.1 Diversification of Berberis ........................................................................................ 40 4.2 Phylogenetic Relationships in Berberis and Divergence time Estimates .................. 45 4 5. Conclusion ....................................................................................................................... 49 6. References ....................................................................................................................... 50 7. Appendices ...................................................................................................................... 61 7.1 Appendix 1 – accesion details ................................................................................... 61 7.2 Appendix 2 – ITS tree ............................................................................................... 64 7.3 Appendix 3 – ndhF tree ............................................................................................. 65 7.4 Appendix 6 – Bayesian tree with all South American species .................................. 66 5 LIST OF FIGURES Figure 1. Distribution of occurrence records for Neotropical Berberis from the Global Biodiversity Information Facility (GBIF).. ......................................................................... 20 Figure 2. Combined bayesian 50% majority rule consensus tree obtained from ndhF and ITS sequences of 102 accessions representing 94 species of Berberis.. ............................. 29 Figure 3. Combined Maximum clade credibility chronogram for combined ITS and ndhF obtained in Beast analysis. .................................................................................................. 31 Figure 4. Prior and posterior probability of models with different number of shifts for Berberis dataset.. ................................................................................................................. 33 Figure 5. Evidence of shifts occurring along Berberis branchs according to BAMM.. ..... 35 Figure 6. phylorate plots for speciation showing the two distinct shift configurations within the 95% credible shift set. ........................................................................................ 36 Figure 7. Macroevolutionary cohort matrix for speciation rates in Berberis Derived from BAMM analysis. ................................................................................................................. 37 Figure 8. Histograms of relative rates of speciation for Berberis clades. .......................... 38 Figure 9. Speciation rates through time of Berberis compared with lineages of interest. black line indicates the mean speciation rate at any indicated time across Berberis. ......... 39 Figure 10. bayesian 50% majority rule consensus tree obtained from ITS sequences of Berberis.. ............................................................................................................................. 64 Figure 11. bayesian 50% majority rule consensus tree obtained from ndhF sequences of Berberis. .............................................................................................................................. 65 Figure 12. Combined bayesian 50% majority rule consensus tree obtained from ndhF and ITS sequences of 116 accessions representing 108 species of Berberis.. ........................... 66 6 LIST