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Phylogeny and Evolution of the Heterobranchia (Mollusca, Gastropoda)

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Phylogeny and Evolution of the Heterobranchia (Mollusca, Gastropoda) Phylogeny and Evolution of the Heterobranchia (Mollusca, Gastropoda) Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften vorgelegt beim Fachbereich Biowissenschaften (FB15) der Johann Wolfgang Goethe – Universität in Frankfurt am Main von Angela Dinapoli aus Mannheim Frankfurt am Main 2009 (D30) Vom Fachbereich Biowissenschaften der Johann Wolfgang Goethe – Universität als Dissertation angenommen Dekan: Prof. Dr. Volker Müller Gutachter: Prof. Dr. Annette Klussmann-Kolb und Prof. Dr. Bruno Streit Datum der Disputation: 13.07.09 Die Schnecke kann dir mehr über den Weg erzählen als der Hase. Bernd Stromberg Table of contents Table of contents List of figures .............................................................................................................................. I List of tables ............................................................................................................................. III List of appendices ..................................................................................................................... IV List of abbreviations (in alphabetical order) ............................................................................. V Zusammenfassung .................................................................................................................... VI Abstract .................................................................................................................................... XI 1. General introduction ....................................................................................................... 1 2. A priori evaluation of data quality .............................................................................. 5 2.1 Introduction ............................................................................................................... 5 2.2 Material and methods ................................................................................................ 8 2.3 Results ..................................................................................................................... 13 2.3.1 A priori evaluation of data quality by the identification of random similarity within sequence alignments using Aliscore and by visual judgement ............. 13 2.3.2 A priori evaluation of data quality by the measurement of substitution saturation in the aligned nucleotide sequences ................................................ 16 2.3.2.1 Index to measure substitution saturation (by Xia et al. 2003) ...................... 16 2.3.2.2 Plotting patristic distances against distances obtained with different models of sequence evolution (graphically) ............................................................. 17 2.3.3 A priori evaluation of data quality by a variety of statistical tests ................... 23 2.3.3.1 Base composition ........................................................................................ 23 2.3.3.2 Chi-Square-Test .......................................................................................... 24 2.3.3.3 Relative-Rate-Test ....................................................................................... 25 2.3.3.4 ILD Test ...................................................................................................... 27 2.3.4 A priori evaluation of phylogenetic signal by split network analyses ............. 27 2.3.4.1 SplitsTree .................................................................................................... 27 2.3.4.2 SAMS .......................................................................................................... 32 2.4 Discussion ............................................................................................................... 37 Table of contents 3. Phylogeny of the Heterobranchia ................................................................................ 42 3.1 Introduction ............................................................................................................. 42 3.2 Material and methods .............................................................................................. 45 3.3 Results ..................................................................................................................... 46 3.4 Discussion ............................................................................................................... 49 4. Evolution of the Heterobranchia ................................................................................. 66 4.1 Introduction ............................................................................................................. 66 4.2 Material and methods .............................................................................................. 68 4.3 Results ..................................................................................................................... 69 4.4 Discussion ............................................................................................................... 73 5. A posteriori evaluation of data quality ......................................................................... 78 5.1 Introduction ............................................................................................................. 78 5.2 Material and methods .............................................................................................. 80 5.3 Results ..................................................................................................................... 83 5.3.1 A posteriori evaluation to test the congruence between the phylogenetic inference and data quality ................................................................................ 83 5.3.1.1 Relative-Rate-Test ....................................................................................... 83 5.3.1.2 Approximately Unbiased (AU) Test ........................................................... 84 5.3.1.3 SplitsTree .................................................................................................... 84 5.3.1.4 SAMS .......................................................................................................... 88 5.3.2 Utility of the secondary structure of 18S rRNA for phylogenetic inference of the Heterobranchia ........................................................................................... 89 5.3.2.1 Secondary structure reconstruction of 18S rRNA ........................................ 90 5.3.2.2 Comparative tree reconstruction of 18S rDNA (with the software MrBayes and Phase) .................................................................................................... 95 5.3.3 Utility of the secondary structure of 28S rRNA for phylogenetic inference of the Heterobranchia ........................................................................................... 97 5.3.3.1 Secondary structure reconstruction of 28S rRNA ........................................ 98 5.3.3.2 Comparative tree reconstruction of 28S rDNA (with the software MrBayes and Phase) .................................................................................................. 104 5.4 Discussion ............................................................................................................. 106 6. General conclusion ...................................................................................................... 115 6.1 New insights into heterobranch phylogeny and evolution ..................................... 115 6.2 Novel methodological approaches using newly invented software ....................... 117 Table of contents 7. Outlook ......................................................................................................................... 121 7.1 Inclusion of additional taxa ................................................................................... 121 7.2 Utility of novel analysing tools ............................................................................. 122 7.3 Novel phylogenetic markers .................................................................................. 122 References .............................................................................................................................. 124 Acknowledgments .................................................................................................................. 139 Appendix ................................................................................................................................ 141 Curriculum vitae Erklärung List of figures I List of figures Fig. 2.1: Consensus profile of the Aliscore check for random similar characters of a: 18S rDNA, b: 28S rDNA and c: 16S rDNA..............................................14 Fig. 2.2: Consensus profile of the Aliscore check for random similar characters of a: COI first codon position, b: COI second codon position and c: COI third codon position................................................................................15 Fig. 2.3: Saturation of substitution of 18S rDNA.............................................................18 Fig. 2.4: Saturation of substitution of 28S rDNA.............................................................19 Fig. 2.5: Saturation of substitution of 16S rDNA.............................................................20 Fig. 2.6: Saturation of substitution of COI position 1.......................................................21 Fig. 2.7: Saturation of substitution of
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