Phylogeny and evolution of the Heterobranchia (Mollusca, Gastropoda) [Elektronische Ressource] / von Angela Dinapoli

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..................