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Phylogenie Und Phylogeographie Eurasischer Viperinae Unter Besonderer Berücksichtigung Der Orientalischen Vipern Der Gattungen Montivipera Und Macrovipera

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Phylogenie Und Phylogeographie Eurasischer Viperinae Unter Besonderer Berücksichtigung Der Orientalischen Vipern Der Gattungen Montivipera Und Macrovipera Phylogenie und Phylogeographie eurasischer Viperinae unter besonderer Berücksichtigung der orientalischen Vipern der Gattungen Montivipera und Macrovipera Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Nikolaus Stümpel aus Braunschweig 1. Referent: apl. Professor Dr. Ulrich Joger 2. Referent: Professor Dr. Miguel Vences eingereicht am: 19.09.2011 mündliche Prüfung (Disputation) am: 19.01.2012 Druckjahr 2012 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Stümpel, N. & U. Joger (2009): Recent advances in phylogeny and taxonomy of Near and Middle Eastern Vipers – an update. – Zookeys 31: 179-191. Tagungsbeiträge Stümpel, N. & U. Joger: “First steps towards a molecular phylogeny of Near- and Middle East Mountain and Blunt-nosed vipers of the genera Montivipera and Macrovipera ” – 2nd Biology of the Vipers conference, 24-27 September 2007, Porto, Portugal Stümpel, N. & U. Joger: “Phylogeny of Near and Middle East Mountain and Blunt-nosed Vipers of the genera Montivipera and Macrovipera inferred by three mitochondrial markers” – 6th World Congress of Herpetology, 17-22 August 2008, Manaus, Brasil Stümpel, N. & U. Joger: “Phylogeny of Near and Middle East Mountain and Blunt-nosed Vipers of the genera Montivipera and Macrovipera inferred by mitochondrial and nuclear markers” – 15th European Congress of Herpetology, 28th September to 2nd October 2009, Kuşadası, Turkey Stümpel, N. & U. Joger: “Phylogeny and molecular clock analyses of west Palearctic Vipers based on complete mitochondrial genomes” – 3rd Biology of the Vipers conference, 31st March-2nd April 2010, Pisa, Italy Für meine lieben Eltern Klaus und Dorothee Stümpel, die mein exotisches Interesse toleriert haben und mich nach Kräften unterstützt haben. Inhalt 1 Vorwort ................................................................................................................................................ 1 2 Material und Methoden ....................................................................................................................... 5 2.1 Probenmaterial .............................................................................................................................. 5 2.1.1 Einleitung ................................................................................................................................ 5 2.1.2 Herkunft des verwendeten Probenmaterials ......................................................................... 6 2.2 Chemikalien, Reagenzien, Kits, Verbrauchsmaterialien und Hilfsmittel ....................................... 7 2.3 Laborgeräte ................................................................................................................................... 8 2.4 Labormethodik .............................................................................................................................. 8 2.4.1 DNA-Isolierung ....................................................................................................................... 8 2.4.2 PCR Methoden........................................................................................................................ 9 2.4.2.1. Auswahl der Markergene ............................................................................................... 9 2.4.2.2 Primerdesign ................................................................................................................. 13 2.4.2.3 Amplifizierung proteincodierender mt-Gene ................................................................ 15 2.4.2.4 Amplifizierung vollständiger mt-Genome mit Hilfe der long and accurate PCR ........... 16 2.4.2.5 Amplifizierung von Kerngenen ...................................................................................... 21 2.4.2.6 Aufreinigung der PCR-Produkte .................................................................................... 24 2.4.3 DNA-Sequenzierung ............................................................................................................. 24 2.4.3.1 Cycle-Sequencing (Sanger Reaktion) ............................................................................. 25 2.4.3.2 Aufreinigung der Cycle-Sequencing-Produkte .............................................................. 25 2.4.3.3 Sequenzierung und Assembling .................................................................................... 26 2.5 Analytische Methoden ................................................................................................................ 26 2.5.1 Alignments ............................................................................................................................ 26 2.5.2 Annotation der Mitogenome ............................................................................................... 28 2.5.3 Stammbaumrekonstruktion und -validierung ...................................................................... 29 2.5.3.1 Sättigungsanalysen ........................................................................................................ 29 2.5.3.2 Berechnung des Evolutionsmodells .............................................................................. 31 2.5.3.3 Wahl der Außengruppen ............................................................................................... 32 2.5.3.4 Evaluation von Stammbäumen („Branch-support“) ..................................................... 32 2.5.3.5 Rekombinationsanalyse ................................................................................................ 33 2.5.3.6 Kongruenz-Test verschiedener Topologien ................................................................... 34 2.5.3.7 Maximum Parsimonie (MP) ........................................................................................... 34 2.5.3.8 Maximum Likelihood (ML) ............................................................................................. 35 2.5.3.9 Bayesianische Inferenz (BI) ............................................................................................ 36 2.5.4 Phylogeographie ................................................................................................................... 37 2.5.5 Kalibrierung einer molekularen Uhr ..................................................................................... 38 2.5.6 Dispersal-Vicariance-Analyse ............................................................................................... 44 2.5.7. Historische Populationsdemographie ................................................................................. 44 3 Phylogenie der Viperinae auf Basis vollständiger mt-Genome .......................................................... 46 3.1 Einleitung ..................................................................................................................................... 46 3.2 Ergebnisse ................................................................................................................................... 49 3.2.1 Sequenz- und Sättigungsanalyse .......................................................................................... 49 3.2.2 Bayesianische Phylogenie ..................................................................................................... 51 3.2.3 mt-Genomorganistation der Viperinae ................................................................................ 54 3.3 Diskussion .................................................................................................................................... 57 4 Divergenzzeiten der Viperinae auf der Basis vollständiger mt-Genome ........................................... 64 4.1 Einleitung ..................................................................................................................................... 64 4.2 Ergebnisse ................................................................................................................................... 67 4.2.1 Auswirkung verschiedener „Relaxed-clock-models“ und „Tree-priors“ auf die Knotendivergenzzeiten .................................................................................................................. 67 4.2.2 Divergenzzeiten der Amnioten ............................................................................................. 70 4.3 Diskussion .................................................................................................................................... 73 5 Phylogenie eurasischer Viperinae ...................................................................................................... 81 5.1 Einleitung ..................................................................................................................................... 81 5.2 Ergebnisse ................................................................................................................................... 84 5.2.1 Sequenz- und Sättigungsanalyse .......................................................................................... 84 5.2.2 Phylogenie auf Basis konkatenierter Mitochondrien- und Kerngene .................................. 86 5.2.3 Phylogenie auf Basis von Kerngenen...................................................................................
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