Diversification and the patterns of introgression in a clade of Neotropical trees Rowan John Schley A thesis submitted for the degree of Doctor of Philosophy at Imperial College London, Department of Life Sciences 1 Thesis abstract The evolutionary processes that led to the assembly of the diverse Neotropical tree flora are complex and poorly understood. It remains unclear at what pace this superlative diversity was accumulated, as do the causes of poor phylogenetic resolution and gene tree incongruence, which are commonly found when reconstructing the phylogeny of rainforest tree species. In addition, the role that introgression has played in the diversification of Neotropical trees and its effect on phylogeny remains enigmatic. The Brownea clade (Leguminosae) are a group of tree species characteristic of Neotropical rainforests, and so serve as an excellent study group with which to approach questions about the diversification of Neotropical trees. This investigation aimed to infer the rates of diversification and biogeographical history of the Brownea clade following the estimation of a phylogenetic tree for the group. The relationships between species within Brownea were then examined using phylogenomic methods to quantify gene tree incongruence, and phylogenetic model testing was used to ascertain whether this incongruence was better explained by incomplete lineage sorting (ILS) or introgression. Finally, two Brownea species found in sympatry were used to examine the impact of introgression on divergence, and whether species boundaries are maintained despite gene flow. More specifically, this study assessed whether genomic loci differed in the degree to which they introgress when compared to the genome-wide average, which would be expected if species boundaries were being maintained by selection. Furthermore, loci which were candidate regions for selection, and those associated with different aspects of the environment and morphology, were inferred in order to determine possible factors maintaining the divergence between the two species. 2 Declaration I confirm that the research presented in this document is my own work, and includes no work done in collaboration with or by others, unless explicitly stated. The co-authors of manuscripts that have been prepared for submission or submitted during the thesis writing process have been acknowledged on pages 3 and 4. The copyright of this thesis rests with the author. Unless otherwise indicated, its contents are licensed under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 International Licence (CC BY-NC-ND). Under this licence, you may copy and redistribute the material in any medium or format on the condition that; you credit the author, do not use it for commercial purposes and do not distribute modified versions of the work. When reusing or sharing this work, ensure you make the licence terms clear to others by naming the licence and linking to the licence text. Please seek permission from the copyright holder for uses of this work that are not included in this licence or permitted under UK Copyright Law. Chapter 2 This chapter has been adapted from the following manuscript, published in Molecular Phylogenetics and Evolution in 2018: Schley R.J., de la Estrella M., Pérez-Escobar O.A., Bruneau A., Barraclough T., Forest F., Klitgård B. (2018) ‘Is Amazonia a 'museum' for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae)’ Molecular Phylogenetics and Evolution, Vol: 126, Pages: 279-292, ISSN: 1055-7903. DOI: https://doi.org/10.1016/j.ympev.2018.04.029. I performed all labwork including DNA extraction, PCR and sequencing for all samples excluding the sequences provided by Dr Karen Redden and those downloaded from NCBI GenBank 3 (http://www.ncbi.nlm.nih.gov/genbank). I performed all data analysis and wrote the manuscript and chapter with feedback from co-authors. Chapter 3 This chapter has been adapted from a manuscript being prepared for submission, authored by Rowan Schley, Manuel de la Estrella, Oscar Alejandro Pérez-Escobar, Timothy Barraclough, Félix Forest and Bente Klitgård. I performed all labwork including DNA extraction, library preparation and sequencing for all samples. I performed all data analysis and wrote the manuscript and chapter with feedback from co-authors. Chapter 4 This chapter has been adapted from a manuscript being prepared for submission, authored by Rowan Schley, Andrew Helmstetter, Renato Valencia, Ben Turner, Timothy Barraclough, Félix Forest and Bente Klitgård. I collected all samples in Yasuní national park unless otherwise stated, performed all labwork including DNA extraction and ddRAD library preparation, and sequencing was performed at an external centre (the Norwegian Sequencing Centre, https://www.sequencing.uio.no). Yasuní soil chemistry data were collected by Dr Benjamin Turner from the Smithsonian Tropical Research Institute (https://www.stri.si.edu) and Dr Renato Valencia (director of the 50 ha plot in Yasuní National Park) from the Pontificia Universidad Católica del Ecuador (https://www.puce.edu.ec/). I performed all data analysis and wrote the manuscript and chapter with feedback from co-authors. 4 Table of Contents Thesis Abstract ...................................................................................................................................... 2 Declaration............................................................................................................................................. 3 Table of Contents .................................................................................................................................. 5 List of Tables ......................................................................................................................................... 9 List of Figures ...................................................................................................................................... 10 Chapter 1: Thesis Introduction ............................................................................................ 11 1.1: The biological diversity of the Neotropics ................................................................................. 11 1.2: Drivers of diversification in the Neotropics ............................................................................... 12 1.2.1: Time and area ............................................................................................................... 12 1.2.2: Geography .................................................................................................................... 13 1.2.3: Ecology ......................................................................................................................... 16 1.3: Speciation and phylogeny .......................................................................................................... 19 1.3.1: Modes of speciation ...................................................................................................... 19 1.3.2: Coalescence and incomplete lineage sorting ............................................................... 21 1.3.3: Hybridization and introgression ................................................................................... 22 1.4: Study system: The Brownea clade ............................................................................................. 24 1.5: Aims ........................................................................................................................................... 27 1.6: Thesis outline ............................................................................................................................. 27 Chapter 2: Is Amazonia a ‘Museum’ or ‘Cradle’ for Neotropical Trees? ....................... 29 2.1: Abstract ...................................................................................................................................... 29 5 2.2: Introduction ............................................................................................................................... 29 2.3: Materials and Methods ............................................................................................................... 33 2.3.1: Taxon sampling, DNA sequencing and phylogenetic analyses ..................................... 33 2.3.2: DNA extraction and sequencing ................................................................................... 35 2.3.3: Phylogenetic analyses and divergence dating ............................................................... 36 2.3.4: Diversification rate analyses ........................................................................................ 37 2.3.5: Ancestral range estimation ............................................................................................ 39 2.4: Results ....................................................................................................................................... 40 2.4.1: Phylogenetic relationships and divergence time estimates ........................................... 40 2.4.2: Diversification rate analyses ........................................................................................ 43 2.4.3: Historical biogeography ................................................................................................ 45 2.5: Discussion ................................................................................................................................. 48