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A Phylogenetic Study of Crepis L. Species Sect. Barkhausia (Asteraceae) Using Low-Copy Nuclear Genes (Gsh1, Sqs) and Plastid Genes (Rps16, Matk1)

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A Phylogenetic Study of Crepis L. Species Sect. Barkhausia (Asteraceae) Using Low-Copy Nuclear Genes (Gsh1, Sqs) and Plastid Genes (Rps16, Matk1) A phylogenetic study of Crepis L. species sect. Barkhausia (Asteraceae) using low-copy nuclear genes (gsh1, sqs) and plastid genes (rps16, matK1) Inaugural-Dissertation in partial fulfilment of the requirements for the degree Doctor of Science (Dr. rer. nat.) Submitted to the Institute of Botany, Justus-Liebig-University Giessen By Ghalia A. Y. Esklual From Benghazi, Libya Giessen 2017 Reviewers: Prof. Dr. Volker Wissemann Special Botany Work Group, Institute of Botany Justus-Liebig-University Giessen Heinrich-Buff-Ring 38 35392 Giessen PD. Dr. Birgit Gemeinholzer Special Botany Work Group, Institute of Botany Justus-Liebig-University Giessen Heinrich-Buff-Ring 38 35392 Giessen Examiners: Prof. Dr. Adriaan Dorresteijn Institute of Developmental Biology of Animals Justus-Liebig-University Giessen Stephanstr. 24, 35390 Giessen Prof. Dr. Sylvia Schnell Institute of Applied Microbiology Justus-Liebig-University Giessen Heinrich-Buff-Ring 26-32 35392 Giessen Date of defence: 20 February 2017 “Ignorance will come to an end when everything is presented as it actually is, and when knowledge about everything is available to each person in the manner that suits him or her.” Muammar Al-Gaddafi from The Green Book, 1976 Dedication TO my father, mother and husband A B C D E F Crepis L. species’ photos: A) C. foetida L., Photographer: Michael Kesl, 2010 on http://www.biolib.cz; B) C. foetida ssp rhoeadifolia (M. Bieb.) Čelak., Photographer: Jiří Kameníček, 2011 on http://www.biolib.cz; C) C. rubra L., Photographer: Vojtěch Herman, 2001 on http://www.biolib.cz; D) C. zacintha (L.) Loisel., Photographer: Thomas Johansson, on http://angio.bergianska.se; E) C. Pusilla (Sommier) Merxmueller., Photographer: Mifsud S, 2010 on maltawildplants.com; F) C. alpina L., Photographer Jan Thomas Johansson, on http://angio.bergianska.se Contents Abbreviation ............................................................................................ I Glossary .................................................................................................. III Summary ................................................................................................. IV Zusammenfassung.................................................................................. VI 1.Introduction ........................................................................................ 01 1.1.The Organism (Crepis L.) ............................................................... 02 1.1.1.Family, Tribe, Genus ............................................................ 02 1.1.2.Crepis Species Section Barkhausia (Moench.) Enke ........... 04 1.1.3.Geographic Distribution of Crepis species sect. Barkhausia. 04 1.1.4. Taxonomic Treatment of Barkhausia Name ......................... 06 1.2. The Methods .................................................................................. 08 1.2.1.Chloroplast DNA (cpDNA) .................................................... 08 1.2.2.Mitochondrial DNA (mtDNA) ................................................. 09 1.2.3.Nuclear DNA (nDNA) ............................................................ 09 1.2.3.1.Nuclear Ribosomal DNA (nrDNA) ............................. 10 1.2.3.2.Low-Copy Nuclear Genes (LCNGs) .......................... 10 1.3.The Evolution Factors ..................................................................... 12 1.3.1.Natural Selection and Evolution ............................................ 12 1.3.2.Mutation ................................................................................ 13 1.3.3.Gene Drift .............................................................................. 14 1.3.4.Gene Flow ............................................................................. 15 1.3.5.Hybridization ......................................................................... 15 1.4.The Objectives ................................................................................. 17 2.Materials and Methods ....................................................................... 18 2.1. Plant Materials and DNA Samples ................................................. 19 2.2.Chemicals, Solutions, and Equipment ............................................ 19 2.3.DNA Extraction................................................................................. 19 2.4.Agarose Gel Electrophoresis............................................................ 19 2.5.PCRs Amplifications......................................................................... 20 2.5.1.Gamma-glutamylcysteine Synthetase (gsh1).......................... 20 2.5.2.Squalene Synthase (sqs)......................................................... 21 2.5.3.Internal Transcribed Spacer (ITS)............................................ 21 2.5.4.Ribosomal Protein S16 Intron (rps16)...................................... 22 2.5.5.Maturase K (matK1)................................................................. 22 2.6.Large Agarose Gel............................................................................ 23 2.6.1.Gel Extraction.......................................................................... 23 2.7.PCR Cloning..................................................................................... 24 2.8.PCR Products Purification................................................................ 24 2.9.Sequencing....................................................................................... 24 2.9.1.Sequences Alignments........................................................... 24 2.9.2.Function assessment.............................................................. 25 2.10.Phylogenetic Reconstruction Trees 25 2.10.1.Phylogenetic Reconstruction Networks (Reticulation) 25 3.Results............................................................ ..................................... 27 3.1.Newly Designed Primers.................................................................. 28 3.2.Sequences and Alignment............................................................... 28 3.2.1. Gsh1...................................................................................... 28 3.2.2. Sqs........................................................................................ 31 3.2.3. Rps16..................................................................................... 33 3.2.4. MatK1..................................................................................... 33 3.3. Phylogeny........................................................................................ 40 3.3.1. Gsh1...................................................................................... 40 3.3.1.1. Phylogeny of the Entire Gsh1 Dataset ………..……. 40 3.3.1.2. Phylogeny of the Reduced Gsh1 Dataset …………. 43 3.3.2. Sqs ....................................................................................... 46 3.3.2.1. Phylogeny of the Entire sqs Dataset ....................... 46 3.3.2.2. Phylogeny of the Reduced sqs Dataset ……….….. 47 3.3.3. Rps16 .................................................................................... 50 3.3.4. MatK1 ................................................................................... 52 3.3.5. Concatenated Analysis of all Nuclear Sequences ………….. 53 3.3.5.1. Character Evolution and Phylogenetic Signals ……. 55 3.3.6. Phylogenetic Reconstruction of the Combined Plastid 57 Dataset ……………………………………………………………. 3.3.7. Phylogenetic Reconstruction of the Combined Nuclear and Plastid Dataset ...................................................................... 58 3.4. Combined Nuclear Tree Versus Combined Plastid Tree ………….. 60 3.5. Hybridization Network and Reticulate Evolution …………………… 61 4.Discussion ......................................................................................... 64 4.1 Gsh1 and Sqs Sequences .............................................................. 65 4.2. Incongruence Between Nuclear and Plastid Gene Trees .............. 66 4.2.1 Gene Duplication .................................................................. 67 4.2.2. Incomplete Lineage Sorting (ILS) and / or Hybridization ..... 69 4.2.3. Reticulate Evolution ............................................................ 70 4.2.3.1. Extensive Hybridization and Introgression .............. 71 4.3.Taxonomy in the Phylogenetic Context …………………………….. 72 4.4. Strength and Limitation of Low-Copy Nuclear Markers (gsh1 75 and sqs) ............................................................................................. 5. Conclusion and Outlook ................................................................... 76 6. References ........................................................................................ 79 7. Acknowledgement ........................................................................... 94 8. Appendix .......................................................................................... 96 8.1. DNA Samples Information and Chemicals…………………........ 96 8.2. Aligned gsh1 DNA Sequences Matrix ........................................... 101 8.3. Aligned sqs DNA Sequences Matrix ............................................. 109 8.4. Aligned rps16 DNA Sequences Matrix ......................................... 116 8.5. Aligned matK1 DNA Sequences Matrix ........................................ 120 9. Declaration ......................................................................................... 121 A B Abbreviations DNA Deoxyribonucleic acid °C Degree Celsius µl Microgram BGBM Botanical Garden and Botanical Museum bp Base
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