Seed germination and genetic structure of two Salvia species in response to environmental variables among phytogeographic regions in Jordan (Part I) and Phylogeny of the pan-tropical family Marantaceae (Part II). Dissertation Zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat) Vorgelegt der Naturwissenschaftlichen Fakultät I Biowissenschaften der Martin-Luther-Universität Halle-Wittenberg Von Herrn Mohammad Mufleh Al-Gharaibeh Geb. am: 18.08.1979 in: Irbid-Jordan Gutachter/in 1. Prof. Dr. Isabell Hensen 2. Prof. Dr. Martin Roeser 3. Prof. Dr. Regina Classen-Bockhof Halle (Saale), den 10.01.2017 Copyright notice Chapters 2 to 4 have been either published in or submitted to international journals or are in preparation for publication. Copyrights are with the authors. Just the publishers and authors have the right for publishing and using the presented material. Therefore, reprint of the presented material requires the publishers’ and authors’ permissions. “Four years ago I started this project as a PhD project, but it turned out to be a long battle to achieve victory and dreams. This dissertation is the culmination of this long process, where the definition of “Weekend” has been deleted from my dictionary. It cannot express the long days spent in analyzing sequences and data, battling shoulder to shoulder with my ex- computer (RIP), R-studio, BioEdite and Microsoft Words, the joy for the synthesis, the hope for good results and the sadness and tiredness with each attempt to add more taxa and analyses.” “At the end, no phrase can describe my happiness when I saw the whole dissertation is printed out.” CONTENTS | 4 Table of Contents Summary ........................................................................................................................................... 6 Zusammenfassung ........................................................................................................................... 10 Chapter 1: General introduction ....................................................................................................... 14 Part I ........................................................................................................................................................ 15 Seed germination and environmental variability ............................................................................... 15 Genetic diversity and environmental variability ................................................................................. 16 Phytogeographic regions and study area ........................................................................................... 18 Medicinal plants and study species .................................................................................................... 20 Part II ....................................................................................................................................................... 22 Phylogeny and molecular data .......................................................................................................... 22 Nuclear and chloroplast DNA .............................................................................................................. 23 Methods to build and test phylogenetic trees ................................................................................... 24 Taxon sampling, molecular data and the accuracy of phylogenetic analyses .................................... 26 Phylogenies of tropical floras ............................................................................................................. 27 Study species and area ....................................................................................................................... 28 Chapter 2: Local adaptation to different phytogeographic regions: habitat-related variations in seed germination in response to temperature and salinity for two medicinal Salvia species from Jordan .. 31 Abstract ................................................................................................................................................... 32 Introduction ............................................................................................................................................ 33 Material and methods............................................................................................................................. 36 Results ..................................................................................................................................................... 40 Discussion ................................................................................................................................................ 44 Chapter 3: Environmental gradients shape the genetic structure of two medicinal Salvia species in Jordan ............................................................................................................................................. 49 Abstract ................................................................................................................................................... 50 Introduction ............................................................................................................................................ 51 Material and methods............................................................................................................................. 53 Results ..................................................................................................................................................... 60 Discussion ................................................................................................................................................ 66 Conclusions ............................................................................................................................................. 71 CONTENTS | 5 Chapter 4: Phylogeny of the pantropically distributed family Marantaceae ....................................... 70 Abstract ................................................................................................................................................... 73 Introduction ............................................................................................................................................ 74 Material and methods............................................................................................................................. 76 Results ..................................................................................................................................................... 79 Discussion ................................................................................................................................................ 87 Conclusions ............................................................................................................................................. 94 Appendices .............................................................................................................................................. 96 Chapter 5: Synthesis ...................................................................................................................... 110 General Introduction ............................................................................................................................. 111 Implication for biodiversity conservation ............................................................................................. 114 Outlook.................................................................................................................................................. 115 References .................................................................................................................................... 118 Acknowledgements........................................................................................................................ 140 Appendix 1 .................................................................................................................................... 143 Publications of the dissertation ............................................................................................................ 144 Other publications by author ................................................................................................................ 144 Curriculum Vitae ................................................................................................................................... 146 Appendix 2 .................................................................................................................................... 149 Declaration of own contributions to the original articles ..................................................................... 150 Declaration of self-contained work / Eigenständigkeitserklärung ........................................................ 151 SUMMARY | 6 SUMMARY Plant biodiversity is the sum total of all biotic variation from the level of genes to ecosystems. However, the relationship between biodiversity and ecological processes has emerged as a central issue in ecological and environmental sciences during the last decade. Because ecosystems collectively determine the biogeochemical processes that regulate species diversity and distribution, studies investigating the potential ecological consequences on levels of plant diversity have provided valuable