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

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Green lineage or Viridiplantae INTRODUCTION 3 Green algae are distributed worldwide and can be found in almost every habit ranging from polar to tropical marine, freshwater and terrestrial environments and as symbionts (Pröschold and Leliaert 2007). They exhibit a remarkable cytological diversity ranging from the world’s smallest free-living eukaryote known to date Ostreococcus taurii (Derelle et al. 2006), over multicellular filaments and foliose blades, to siphonous life forms that are essentially composed of a single giant cell containing countless nuclei (Fig. 2). Together with land plants, green algae form the green lineage or Viridiplantae (also written as Virideaplantae or known as green plants, Chlorobionta, Chloroplastida or Chlorophycophyta). Morphological and molecular studies have identified a major split within the Viridiplantae giving rise to two monophyletic lineages, the Chlorophyta and the Streptophyta (Pickett-Heaps and Marchant 1972, Lewis and McCourt 2004) (Fig. 3). The streptophytes comprise several lineages of predominantly freshwater green algae (often called charophytes or charophyte green algae) and the land plants (Embryophyta) which evolved roughly 470 million years ago from a charophyte ancestor. The majority of green algae, however, belong to the Chlorophyta. Streptophyta When motile cells are present, the Streptophyta are characterized by biflagellate cells with asymmetrically flagellar roots including a multilayered structure or MLS (a distinct parallel arrangement of microtubules) and a smaller root. In all representatives the nuclear envelope breaks down before the chromosomes separate (open mitosis) and the mitotic spindle is persistent which helps to keep the daughter nuclei separate until cytokinesis has been accomplished. Biochemical characters such as photorespiratory enzymes are different from those found in most chlorophyte green algae (Figs. 4 and 5; Table 1). Several phylogenetic studies have tried to determine the origins of the land plants, focussing on the green algal progenitors of the Streptophyta. Recent studies have indicated the scaly green flagellate Mesostigma as the earliest diverging streptophyte. Initially, the scaly flagellate was placed within the prasinophytes (Mattox and Stewart 1984), later ultrastructural investigations (e.g. a flagellum which is anchored in the cell by means of an asymmetric root) revealed the association with the Streptophyta (Melkonian 1989). Molecular phylogenies also showed conflicting results regarding the phylogenetic relationships of this enigmatic species: Mesostigma either diverges before the Chlorophyta/Streptophyta split (Lemieux et al. 2000, Turmel et al. 2002a, Turmel et al. 2002b) or as an early diverging flagellate within the Streptophyta (Bhattacharya et al. 1998, Marin and Melkonian 1999, Karol et al. 2001). Increasing taxon and gene sampling and the use of more realistic models of evolution provide evidence that Mesostigma is an early diverging lineage within the Streptophyta (Petersen et al. 2006, Lemieux et al. 2007, Rodriguez-Ezpeleta et al. 2007). The colonial soil alga Chlorokybus diverges after Mesostigma in most phylogenies (Karol et al. 2001), although more recent studies united Mesostigma and Chlorokybus as the earliest diverging branch of the Streptophyta (Lemieux et al. 2007). Unbranched filaments that form the class Klebsormidiophyceae diverge next, followed by the Zygnematophyceae clade, which includes unicells and unbranched filaments with isogamous sexual reproduction. The more complex charophytes are Coleochaetophyceae and Charophyceae both consisting of branched filaments with oogamous sexual reproduction. It remains
4 CHAPTER 1 inconclusive from which group of algae Embryophytes emerged. Karol et al. (2001) resolved the stoneworts (Charophyceae) as the closest relatives of the Embryophyta, while evidence from plastid genomes point toward the conjugating algae or Zygnematophyceae (Lemieux et al. 2007). Figure 3. Phylogenetic relationships between green algae inferred from several phylogenetic studies: Streptophyta (Karol et al. 2001: SSU nrDNA, mitochondrial nad5 gene and plastid rbcL and atpB genes), prasinophytes (Guillou et al. 2004: SSU nrDNA), Trebouxiophyceae (Karsten et al. 2005: SSU nrDNA), Chlorophyceae (Turmel et al. 2008: chloroplast genes), Ulvophyceae (Lopez-Bautista and Chapman 2003: SSU nrDNA) and (Watanabe and Nakayama 2007: SSU nrDNA). The main interest of chapter 2 is to resolve relations between Ulvophyceae, Trebouxiophyceae and Chlorophyceae (1) and among Ulvophyceae (2). Representatives from each clade are studied (except those marked in gray).
Page 1 and 2: Phylogeny and molecular evolution o
Page 3 and 4: Promotor: Prof. Dr. O. De Clerck (U
Page 5 and 6: Aan de mensen van de plantkunde in
Page 8 and 9: 1 Introduction Algae Algae are a la
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
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Page 34 and 35: PHYLOGENY OF GREEN ALGAE 27 to the
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Page 38 and 39: Topological hypothesis testing PHYL
Page 40 and 41: Additional files PHYLOGENY OF GREEN
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Page 44 and 45: actin G6PI GapA histone OEE1 40S_S9
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Page 50 and 51: 3 Gain and loss of elongation facto
Page 52 and 53: GAIN AND LOSS OF ELONGATION FACTOR
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Methods Algal strains GAIN AND LOSS
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GAIN AND LOSS OF ELONGATION FACTOR
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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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