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Genetic and Taxonomic Incongruences in Mediterranean Endemic Flora: Four Different Case Studies

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Genetic and Taxonomic Incongruences in Mediterranean Endemic Flora: Four Different Case Studies UNIVERSITÀ DEGLI STUDI DELLA TUSCIA DI VITERBO DIPARTIMENTO DI SCIENZE E TECNOLOGIE PER L'AGRICOLTURA, LE FORESTE, LA NATURA E L'ENERGIA (DAFNE) Corso di Dottorato di Ricerca in Scienze e tecnologie per la gestione forestale e ambientale - XXV Ciclo. Genetic and taxonomic incongruences in Mediterranean endemic flora: four different case studies s.s.d. AGR/05 Tesi di dottorato di : Dott. Tamara Kirin Coordinatore del corso Tutore Prof. Rosanna Bellarosa Prof. Bartolomeo Schirone 7 Maggio 2013 Preface PREFACE The Mediterranean Basin is a region of great biodiversity. Around 10% of all the existing plant species in the world inhabit this small area. This amazing fact provides opportunities for continuous botanical studies and analyses. Long and complex geological history and long-term climate of the Mediterranean offer a vast number of particular microhabitats inhabited by isolated, highly specialised species and subspecies. High genetic richness appears to be another particularity of the area which is still being recognised and investigated. This is why I decided to study genetic variation of four different Mediterranean species complexes. The selected species include herbaceous and woody taxa, as well as Gymnosperms and Angiosperms. European Black Pine ( Pinus nigra Arnold.) and Aleppo Pine ( Pinus halepensis Mill.), ancient gymnosperms, represent two of the core species of the Mediterranean. Despite similarly high importance in habitats they occupy, areas which they inhabit are very different, resulting in different ecology and life-history traits of these two species. European Nettle Tree ( Celtis australis L.), though not exclusively a Mediterranean species, represents an important element of the Mediterranean vegetation and has had an important role for the local inhabitants, from the time of the first settlers till today (alimentary, wood, spiritual and horticultural). Its particularities are also two closely related species ( C. tournifortii Lam. and, so called, C. aethnensis (Tornab.) Strobl) with their unresolved phylogenetic status. The last of the studied taxa is an herbaceous group of plants, Inula verbascifolia group, which represents a complex of strictly Mediterranean plants from which I restricted my analyses on Inulas verbascifolia subsp. verbascifolia taxa. The centre of their distribution is the Ionic Sea and their divergence in an outcome of particular environmental conditions around the Mediterranean costs. I this work I analyzed intra-specific genetic diversity and phylogeography of four species, in order to resolve the existing incongruence in their systematics. By applying various molecular methods and testing various regions of the genome I aimed to provide a Preface comprehensive molecular systematics of the studied species to help and encourage various future studies. Moreover, I applied the same approach in computational genetic analyses, testing different methods and models. I discuss, both, the results and the applicability of all the applied methods. Finally, I introduced a brand new technology called High resolution melting (HRM) to test and, eventually recommend its use, in phylogenetics and phylogeography studies, fields in which it has never been used before. Apart from giving new insights to the phylogenetics of the studied groups, I hope this study will provide an overview of the present molecular techniques and encourage more studies on unresolved evolutionary traits in Mediterranean Basin. At the end, we should never forget the biodiversity loss we are experiencing at the moment. The biodiversity should not be regarded only at the level of species but also on the genetic level. Therefore any study on genetic variability is also a study towards the conservation of some unique identities. Table of Contents TABLE OF CONTENTS 1. INTRODUCTION …………………………………………………………………… 1 1.1. Mediterranean region ……………………………………………………….. 1 1.1.1. Mediterranean Basin and its biodiversity ………………...………. 3 1.1.2. Geology and history of the Mediterranean region …….…………... 4 1.1.3. Pleistocene in the Mediterranean region …………….,…………… 5 1.1.4. Evolution after the Pleistocene and human impact on the vegetation ………………………………………………………… 7 1.2. Studied species ……………………………………………………………… 9 1.2.1. Genus Pinus ……………………………………………………….. 9 1.2.1.1. Evolution of pines ……………………………………….. 9 1.2.1.2. Pines of the Mediterranean Basin ……………………….. 10 1.2.1.3. Genetic diversity of pines ………………………………. 11 1.2.1.4. Systematics of genus Pinus ................................................ 12 1.2.1.5. Aleppo pine ( Pinus halepensis Miller) .............................. 13 1.2.1.6. European black pine ( Pinus nigra Arnold)......................... 18 1.2.2. Genus Celtis ……………………………………………………….. 27 1.2.2.1. European nettle tree ( Celtis australis L.) ……………….. 28 1.2.2.2. Oriental Hackberry (Celtis tournefortii Lam.) …………... 29 1.2.3. Inula verbascifolia subsp. v erbascifolia … ………………………. 29 1.3. Molecular analyses ………………………………………………………….. 32 1.3.1. Discovering the variability and evolutionary Table of Contents history of the species ……………………………………............... 33 1.3.2. Molecular markers used for DNA sequencing …………………….. 36 1.3.3. Molecular phylogenetics ................................................................... 44 2. OBJECTIVES AND SCOPE OF THE STUDY ……………………………………… 50 3. MATERIAL AND METHODS ………………………………………………………. 52 3.1. Sampling ……………………………………………………………………. 52 3.2. Conserving the material ……………………………………………………... 58 3.3 DNA extraction ……………………………………………………………..... 59 3.4. Amplification of the fragment using the PCR machine ……………………. 62 3.5. DNA purification ……………………………………………………………. 64 3.6. DNA fragments verification – Gel electrophoresis ………………………… 65 3.7. DNA sequencing ……………………………………………………………. 66 3.8. Bioinformatics ………………………………………………………………. 66 3.8.1. Chromatogram visualization ………………………………………. 66 3.8.2. Multiple sequence alignment ……………………………………… 67 3.8.3. Mesquite 2.75. …………………………………………………….. 67 3.8.4. DnaSP 5.10. ……………………………………………………….. 68 3.8.5. Mega 5.0. ………………………………………………………...... 68 3.8.6. RAxML ……………………………………………………………. 69 3.8.7. MrBayes …………………………………………………………… 70 3.8.8. Network 4.6.1.1. …………………………………………………....72 Table of Contents 4. RESULTS …………………………………………………………………………….. 74 4.1. Markers applicability ……………………………………………………….. 74 4.1.1. Aleppo Pine ……………………………………………………….. 74 4.1.2. European Black Pine ………………………………………………. 75 4.1.3. European Nettle Tree ……………………………………………… 77 4.1.4. Inula verbascifolia group ………………………………………….. 78 4.1.5. Markers combination ……………………………………………… 79 4.2. Genetic reports between the samples ………………………………………... 81 4.2.1. Aleppo Pine ……………………………………………………….. 81 4.2.2. European Black Pine ………………………………………...…….. 85 4.2.3. European Nettle Tree ……………………………………………… 88 4.2.4. Inula verbascifolia group ………………………………………….. 90 4.3. Genetic position of the studied species ……………………………………... 93 4.3.1. Pines ……………………………………………………………….. 93 4.3.2. Genus Celtis …………………………………………………....... 97 4.3.3. Genus Inula ………………………………………………............. 100 5. DISCUSSION ……………………………………………………………………….. 101 5.1. Choosing a perfect DNA marker ……………………………………….. 101 5.2. Application of the molecular methods for reconstructing of phylogenetic trees ………………..…………………………………... 104 5.3. Phylogenetic results obtained …………………………………………... 105 5.3.1. Aleppo Pine ……………………………………………………… 106 Table of Contents 5.3.2. European Black Pine …………………………………………….. 107 5.3.3. European Nettle Tree …………………………………………….. 109 5.3.4. Inula verbascifolia group ………………………………………… 109 5.4. Additional DNA sequences ………………………………………... 111 6. HIGH RESOLUTION MELTING (HRM) ANALYSES …………………………… 113 6.1. Introduction ..………………………………………………………………. 113 6.2. Material and methods ……………………………………………………… 115 6.3. Results and discussion ................................................................................... 119 6.4. Conclusions ................................................................................................... 127 7. CONCLUSIONS …………………………………………………………………….. 128 8. REFERENCES ……………………………………………….……………………… 130 Introduction 1. INTRODUCTION 1.1. Mediterranean region Mediterranean Basin is the area around the Mediterranean Sea which covers around 2.3 x 10 6 km 2 and stretches over 3 800 km from west to east and 1 000 km from north to south. Especially remarkable is its unusual geographical and topographical diversity with high mountains, wetlands, peninsulas and, one of the largest, archipelagos in the world. All these structures together with favourable climate are contributing in making the Mediterranean Basin such a biodiversity rich region. Natural borders of the Basin are usually mountains but in some parts it is more the climate that makes the distinct confine from the other regions. The mountain chains including the: Pyrenees (dividing Spain from France), the Alps (dividing Italy from Central Europe), the Dinarides (along the eastern Adriatic) and the Balkan and Rhodope Mountains (of the Balkan Peninsula) divide the Mediterranean from the temperate climate regions of Western and Central Europe. Continuing towards east the Basin extends into Western Asia, spreading over the western and southern portions of the Anatolian peninsula. The eastern Mediterranean littoral between Anatolia and Egypt is called the Levant, nowadays consisting of Lebanon, Syria, Jordan, Israel, Palestine, Cyprus, Hatay Province and parts of southern Turkey, regions of northwestern Iraq and the Sinai Peninsula; and is being bounded by the Syrian and Negev deserts. The strip of Mediterranean
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