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Chapter 1. General Introduction Relicts, Refugia and Reticulation: A Study of Population History, Hybrids and Phylogeny in the Long-Lived Flowering Tree Genus Tilia Prattana Phuekvilai Thesis submitted for the degree of Doctor of Philosophy School of Biology Newcastle University July 2014 Declaration I hereby certify that this thesis is the original work of my own. No part of the material has been submitted to the Newcastle University or any other University for obtaining a higher degree. All information derived from other sources has been acknowledged and indicated in the thesis. Prattana Phuekvilai July 2014 i Abstract Tilia L. (lime or basswood) is a genus of large trees that are widely distributed in the temperate regions of the Northern Hemisphere. Tilia is an under-investigated genus with unknown species relationships. Therefore, a phylogeny of the genus was reconstructed. This revealed disagreement of the phylogenetic placement of some species and also indicated extensive hybridization. To investigate this further, the most tractable and widely distributed species across Europe, T. cordata (Mill.) or small leaved lime and T. platyphyllos (Scop.) or large leaved lime, were selected for study. This study aims to increase the understanding of genetic diversity and hybridization between the two Tilia species. Also, to gain insight into postglacial recolonization in Tilia across Europe, the patterns of population genetic structure were investigated. In order to achieve the goals, 15 microsatellite markers were developed for detailed genetic analysis. These loci clearly discriminated the two Tilia species. Cross- amplification results indicated that twelve microsatellite markers amplified polymorphic loci in 24 species in the genus. A high level of polymorphism was observed in twenty- five populations of T. cordata and 15 populations of T. platyphyllos from natural woods across Europe. The level of genetic diversity in T. platyphyllos is higher than in T. cordata. Both microsatellite and morphological analysis revealed that natural hybridisation and introgression have occurred between T. cordata and T. platyphyllos in sympatric UK populations, which could be of importance for adaptation and other evolutionary processes. The partial congruence of molecular and morphological analysis suggests that molecular markers are more reliable than morphological analysis for detecting hybridization. The stronger genetic structure observed in T. platyphyllos than in T. cordata suggested that the migration and colonization in the northern areas of T. cordata occurred before those of T. platyphyllos. Microsatellite analysis suggested different possible colonization routes between the two Tilia species. However, T. cordata and T. platyphyllos seem to share the three main refugia in southern Europe (Iberia, Italy and the Balkans). In addition, T. cordata seems to have additional putative refugia in eastern areas. The haplotype network and some shared haplotypes of eight chloroplast regions indicate incomplete lineage sorting rather than recent hybridization. ii Acknowledgements Firstly, I would like to express my deep gratitude and thanks to my supervisor, Dr Kirsten Wolff for her supervision, encouragement and support throughout the completion of my study. Working with Kirsten for almost four years has been a great privilege. She has taught me how to be a population geneticist. Also, she gave me the opportunity to attend workshops and conferences, which helped me to broaden my perspective and provide me a great experience. She has supported me not only in the academic life, but also provided me opportunities to have experiences outside the University. She is an excellent supervisor who never hesitated to provide any kind of help. This project would never have been accomplished without her. I would like to thanks Prof. Donald Pigott who helped in suggestion of species relationships and provided the samples of most Tilia species used in phylogenetic study. I would also like to express my gratitude to Dr. Paul Ashton and his colleages, who helped both in collecting the samples in the UK and writing the paper. I owe a great deal of thanks to people who helped me collecting the samples across Europe, without whom this study would not have been possible. I am grateful to thanks all of the staff and friends in the School of Biology for their kindness, support and friendship. Special thanks go to Helen Martin for her help with cloning techniques and her advice. I appreciate the assistance of laboratory members, Dr. Nicholas Levsen and Samuel Logan for their useful discussion and assistance in my project. I gratefully acknowledge the Royal Thai Government for providing me with a PhD scholarship. I would also like to thank to the staff at the Office of Educational Affairs (OEA) in London for their help and support. I also wish to thanks the members of the Thai Society in Newcastle for their sincere friendships. Finally, I would like to express my deepest appreciation to my parents and sister for their love, support, understanding and encouragement. I would like to dedicate this achievement to them. iii Publications Related to the Thesis Publication: Phuekvilai P, Wolff K (2013). Characterization of microsatellite loci in Tilia platyphyllos (Malvaceae) and cross-amplification in related species. Applications in Plant Sciences 1(4): 1200386. Oral presentations: Phuekvilai P (2012). Evolution and population genetics in the genus Tilia. Ecological Genetics Group Conference, Edinburgh, UK. Phuekvilai P (2014). Population structure and phylogeography of Tilia cordata and T. phythyllos across Europe. Ecological Genetics Group Conference, Newcastle, UK. Poster presentations: Phuekvilai P, Wolff K (2011). Evolution and population genetics in the genus Tilia. Ecological Genetics Group Conference, London, UK. Phuekvilai P, Wolff K (2012). Genetic diversity in ancient lime trees. Trees Beyond the Wood Conference, Sheffield, UK. Phuekvilai P, Wolff K (2013). Genetics diversity and population structure in T. cordata and T. platyphyllos. Ecological Genetics Group Conference, Belfast, UK. iv Table of contents Declaration…………………………………………………………………….…………i Abstract………………………………………………………………………………….ii Acknowledgements……………………………………………………………………..iii Publications Related to the Thesis………………..……………………………………..iv Table of Contents……………………………………………………………...…………v List of Figures…………………………………………………………………….…......ix List of Tables……………………………………………………………………….......xii Chapter 1. General introduction ................................................................................... 1 1.1 Genetic diversity ...................................................................................................... 1 1.2 Factors influencing extent and distribution of genetic diversity ............................. 1 1.3 Tree diversity and their importance ......................................................................... 2 1.4 The genus Tilia and its distribution ......................................................................... 3 1.5 Importance and uses of Tilia ................................................................................... 6 1.5.1 Biodiversity value ............................................................................................. 6 1.5.2 Human value ..................................................................................................... 7 1.6 Approach and aims of research ............................................................................... 7 Chapter 2. Phylogenetic analysis of the genus Tilia ................................................... 10 2.1 Abstract ................................................................................................................. 10 2.2 Introduction ........................................................................................................... 10 2.2.1 Phylogenetic utility of chloroplast DNA ........................................................ 11 2.2.2 Phylogenetic utility of nuclear ribosomal DNA ............................................. 12 2.2.3 Phylogenetic utility of nuclear genes .............................................................. 13 2.2.4 Nuclear genes used in this study ..................................................................... 13 2.2.5 Taxonomic history of Tilia ............................................................................. 15 2.3 Materials and methods ........................................................................................... 18 2.3.1 Species sampling............................................................................................. 18 2.3.2 DNA extraction ............................................................................................... 20 2.3.3 Chloroplast amplification and sequencing ...................................................... 20 2.3.4 Nuclear amplification and sequencing ............................................................ 21 v 2.3.5 Nuclear gene cloning ...................................................................................... 23 2.3.6 Sequence alignment and phylogenetic analysis .............................................. 23 2.4 Results ................................................................................................................... 24 2.4.1 Characteristics of chloroplast, nuclear DNA and ITS rDNA sequences ........ 24 2.4.2 Phylogenetic analysis ...................................................................................... 27 2.5 Discussion
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