Phylogeny and molecular evolution of green algae - Phycology ...

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Universiteit Gent Faculteit Wetenschappen, Vakgroep Biologie Onderzoeksgroep Algologie Phylogeny and molecular evolution of green algae Fylogenie en moleculaire evolutie van groenwieren Ellen Cocquyt Proefschrift voorgelegd tot het behalen van de graad van Doctor in de Wetenschappen: Biologie Academiejaar 2008-2009
Promotor: Prof. Dr. O. De Clerck (Universiteit Gent) Co-promotor: Dr. H. Verbruggen (Universiteit Gent) Leden van de leescommissie: Prof. Dr. K. Hoef-Emden (Universität zu Köln, Germany) Dr. P. Rouzé (Universiteit Gent) Prof. Dr. A. Vanderpoorten (Université de Liège) Overige leden van de examencommissie: Prof. Dr. K. Sabbe (Universiteit Gent) Prof. Dr. Erik Smets (Katholieke Universiteit Leuven and National Herbarium of the Nederlands) Prof. Dr. W. Vyverman (Universiteit Gent) Photographs cover: Frederik Leliaert and Heroen Verbruggen Photographs upper band, from left to right and from top to bottom: Boodlea, Phyllodictyon, Dictyosphaeria, Ulva, Cladophora and Valonia Photographs lower band, from left to right: Boergesenia, Codium, Halimeda, Dictyosphaeria and Cladophora Photographs at the back, from left to right and from top to bottom: Blastophysa, Trentepohlia, Ignatius and Chlamydomonas The research reported in this thesis was funded by the Special Research Fund (Ghent University, DOZA-01107605) and performed in the Research Group Phycology and the Center for Molecular Phylogenetics and Evolution, Biology Department, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium. www.phycology.ugent.be
Page 1: Phylogeny and molecular evolution o
Page 5 and 6: Aan de mensen van de plantkunde in
Page 8 and 9: 1 Introduction Algae Algae are a la
Page 10 and 11: Green lineage or Viridiplantae INTR
Page 12 and 13: INTRODUCTION 5 Figure 4. Variation
Page 14 and 15: INTRODUCTION 7 (shared gene losses
Page 16 and 17: INTRODUCTION 9 Sphaeropleales (dire
Page 18 and 19: INTRODUCTION 11 Figure 7. The estim
Page 20 and 21: Tree building methods Maximum likel
Page 22 and 23: INTRODUCTION 15 Figure 9. Flow char
Page 24 and 25: Removal of fast-evolving sites INTR
Page 26 and 27: 2 Ancient relationships among green
Page 28 and 29: PHYLOGENY OF GREEN ALGAE 21 environ
Page 30 and 31: PHYLOGENY OF GREEN ALGAE 23 Our phy
Page 32 and 33: PHYLOGENY OF GREEN ALGAE 25 Figure
Page 34 and 35: PHYLOGENY OF GREEN ALGAE 27 to the
Page 36 and 37: PHYLOGENY OF GREEN ALGAE 29 primers
Page 38 and 39: Topological hypothesis testing PHYL
Page 40 and 41: Additional files PHYLOGENY OF GREEN
Page 42 and 43: PHYLOGENY OF GREEN ALGAE 35 Figure
Page 44 and 45: actin G6PI GapA histone OEE1 40S_S9
Page 46 and 47: PHYLOGENY OF GREEN ALGAE 39 atpB rb
Page 48 and 49: PHYLOGENY OF GREEN ALGAE 41 Table S
Page 50 and 51: 3 Gain and loss of elongation facto
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GAIN AND LOSS OF ELONGATION FACTOR
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Methods Algal strains GAIN AND LOSS
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Authors' contributions GAIN AND LOS
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Additional file 2 GAIN AND LOSS OF
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Additional file 4 GAIN AND LOSS OF
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Additional file 6 Table S2. GenBank
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atpB rbcL SSU rDNA EF-1α EFL Chlor
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atpB rbcL SSU rDNA EF-1α EFL choan
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4 Complex phylogenetic distribution
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NON-CANONICAL GENENTIC CODE 71 addi
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Figure 1. The occurrence of a non-c
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NON-CANONICAL GENENTIC CODE 75 Figu
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Multiple independent gains NON-CANO
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Acknowledgements NON-CANONICAL GENE
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82 CHAPTER 5 Introduction The genet
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84 CHAPTER 5 The goal of this study
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86 CHAPTER 5
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88 CHAPTER 5 Codon usage bias and G
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6 A multi-locus time-calibrated phy
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A MULTI-LOCUS TIME-CALIBRATED PHYLO
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Time-calibrated phylogeny A MULTI-L
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Acknowledgments A MULTI-LOCUS TIME-
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Dichotomosiphon tuberosus AB038487
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Table 3. List of calibration points
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116 CHAPTER 7 Introduction Green al
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118 CHAPTER 7 ulvophycean order Ulo
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120 CHAPTER 7 10). Filaments that w
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122 CHAPTER 7 invaded freshwater ha
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124 CHAPTER 7 filaments, and the po
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126 CHAPTER 7 Type species: Okellya
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8 General discussion This thesis fo
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SSU nrDNA phylogenies GENERAL DISCU
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GENERAL DISCUSSION 133 copy nuclear
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GENERAL DISCUSSION 135 Figure 2. Su
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GENERAL DISCUSSION 137 Our site str
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GENERAL DISCUSSION 139 In the light
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GENERAL DISCUSSION 141 genomes (Rok
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144 REFERENCES Bartsch I and Kuhlen
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146 REFERENCES Derelle E, Ferraz C,
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148 REFERENCES Hanyuda T, Wakana I,
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150 REFERENCES Knight RD, Freeland
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152 REFERENCES Mattox K and Stewart
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154 REFERENCES Philippe H, Lartillo
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156 REFERENCES Sanderson MJ. 2002.
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158 REFERENCES Turmel M, Otis C, an
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160 REFERENCES Zechman FW, Theriot
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162 SUMMARY derived from a multinuc
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Samenvatting Groenwieren worden wer
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SAMENVATTING 167 kleine variaties o
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