Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2012 The evolution of morphological complexity in cyanobacteria Schirrmeister, Bettina E Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-164190 Dissertation Published Version Originally published at: Schirrmeister, Bettina E. The evolution of morphological complexity in cyanobacteria. 2012, University of Zurich, Faculty of Science. THE EVOLUTION OF MORPHOLOGICAL COMPLEXITY IN CYANOBACTERIA Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultät der Universität Zürich von Bettina E. Schirrmeister aus Deutschland Promotionskomitee Prof. Dr. Homayoun C Bagheri (Leiter der Dissertation) Prof. Dr. Lukas Keller Prof. Dr. Kentaro K Shimizu Zürich, 2012 BETTINA E. SCHIRRMEISTER DISSERTATION The Evolution of Morphological Complexity in Cyanobacteria Author: Supervisor: Bettina E. SCHIRRMEISTER Prof.Dr. Homayoun BAGHERI February 21, 2012 Contents Summary xiii Zusammenfassung xvii INTRODUCTION: A brief history of cyanobacterial phylogenetics 1 On Phylogenetic trees . 3 History of a tree (1739-1900) . 3 Mendelians and biometricians (1900-1918) . 7 Population genetics and the evolutionary synthesis (1918-1950) . 7 Cladistics . 8 Molecular biology . 9 On Cyanobacteria . 10 A phylum with variable notations . 10 The taxonomy of blue green algae . 11 The phylogenetic relation of blue green algae . 13 Classification of prokaryotes . 14 Bergey’s Manual of Systematic Bacteriology . 15 The international code of nomenclature for cyanobacteria . 16 Cyanobacterial ancestry . 18 Molecular phylogenetics of cyanobacteria . 18 Where is cyanobacterial phylogenetics going? . 19 CHAPTER I: Gene copy number variation and its significance in cyanobacterial phylogeny 23 Background . 25 Results and Discussion . 27 Identification of conserved gene copies and their phylogenetic relevance . 27 Strong conservation of 16S rRNA copies . 31 Evolution of 16S rRNA gene copies in cyanobacteria . 35 Conclusion . 36 Methods . 37 iv Contents Data choice and description . 37 Identification of conserved paralogs and correlation to morphotypes . 37 Phylogenetic analyses . 38 Molecular distance analyses . 39 CHAPTER II: The origin of multicellularity in cyanobacteria 41 Background . 43 Results and Discussion . 45 Phylogenetic analyses . 45 Ancestral character state reconstruction . 52 Gaining and losing multicellularity . 56 Prokaryotic fossil record before the “Great Oxygenation Event”: Evidence for multicellular cyanobacteria? . 57 Conclusion . 60 Methods . 61 Taxon sampling . 61 Phylogenetic analyses . 61 Ancestral character state reconstruction . 63 CHAPTER III: Evolution of cyanobacterial morphotypes: Taxa required for improved phyloge- nomic approaches 67 CHAPTER IV: Evolution of multicellularity coincided with increased diversification of cyanobac- teria and the Great Oxidation Event 75 Introduction . 77 Results . 77 Phylogenetic analyses. 78 Divergence time estimation . 79 Shifts in Diversification Rates . 79 Discussion . 80 Evolution of multicellularity and possible consequences . 80 Early Earth history and the fossil record . 82 Conclusion . 83 Methods . 84 Taxon sampling . 84 Alignment and Phylogenetic analyses . 84 Divergence time estimation . 84 Calibration points . 85 Shifts in Diversification Rates . 86 Contents v CONCLUSION 89 Bibliography 91 Additional Files 113 Additional Files to chapter I: Gene copy number variation and its significance in cyanobacterial phy- logeny. 114 1.1 - Identified gene copies . 114 1.2 - 16S rRNA gene copy data including data from the rrndb-database . 127 1.3 - Distribution of 16S rRNA copy numbers using additional data from rrndb . 128 1.4 - Distribution of mean distances within species from bootstrap samples for the different eubacterial phyla . 129 1.5 - Distribution of mean distances between species from bootstrap samples for the different eubacterial phyla . 130 1.6 - Phylogenetic tree and distance matrix of Spirochaetes . 131 1.7 - Phylogenetic tree of Bacteroidetes . 132 1.8 - Distance matrix of Bacteroidetes . 133 1.9 - Distance matrix of cyanobacterial ITS-region . 134 1.10 - Data of 16S rRNA gene sequences of the different eubacterial phyla . 135 Additional Files to chapter II: The origin of multicellularity in cyanobacteria . 136 2.1 - Taxon names of the phylogenetic tree of cyanobacteria . 136 2.2 - Phylogenetic tree of cyanobacteria - newick format . 149 2.3 - Rooted Bayesian consensus tree of 27 eubacterial species including five cyanobacterial species150 2.4 - Bayesian consensus trees of cyanobacterial subset and different outgroups - newick format 151 2.5 - Results from the test of substitutional saturation . 152 2.6 - Maximum likelihood tree of cyanobacterial subset . 152 2.7 - Ancestral character state reconstruction using maximum parsimony . 154 Additional Files to chapter IV: Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event . 155 4.1 - Bayesian consensus tree. 156 4.2 - Bayesian consensus tree of BEAST-analysis 7 . 157 4.3 - Estimated clade specific diversification rates using species numbers. 158 4.4 - Estimated clade specific diversification rates using strain numbers. 159 4.5 - Estimated ages of nodes found in the Bayesian consensus trees for each analysis. 160 4.6 - Names of taxa, accession numbers and number of species and strains . 161 4.7 - Results of clade specific diversification rate estimation for eight different analyses. 162 4.8 - Nucleotide sequence of G40R . 163 Additional Publications 164 vi Contents The evolutionary path to terminal differentiation and division of labor in cyanobacteria . 165 Acknowledgements 179 Curriculum vitae 186 List of Figures 0.1 Scala naturae ..