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

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PHYLOGENY OF GREEN ALGAE 21 environment, which involves profound physiological adaptation (Mann 1996, Becker and Marin 2009). Furthermore, marine versus freshwater lifestyles coincide with differentiations in life-style: whereas the marine Ulvophyceae have a haplodiplontic life cycle with alternating generations of free-living gametophyte and sporophyte phases and sporic meiosis, freshwater green algae predominantly have a haploid vegetative phase and a single-celled, often dormant zygote as the diploid stage (haplontic life cycle with zygotic meiosis) (Lewis and McCourt 2004). Resolving the branching order among the three classes can help to understand the diversification of ecological, physiological and life history features of the UTC clade. Whereas Prasinophyceae are unicellular marine plankton and Trebouxiophyceae and Chlorophyceae are unicells, colonies or in a few cases simple filaments, the predominantly marine class Ulvophyceae has evolved an unrivalled diversity of morphologies and cytological types. Morphologies in the class range from simple unicells to multicellular organisms of various levels of complexity (the green seaweeds). Cytological diversity is equally diverse and ranges from uni- to multinucleate cells and, in the extreme, giant tubular cells with millions of nuclei. Five major groups are recognized in the Ulvophyceae. The first has fairly typical cells and ranges in morphology from unicells to multicellular filaments and sheets, the multicellular types being more derived (orders Oltmannsiellopsidales, Ulvales and Ulotrichales) (Cocquyt et al. 2009). The second group has similar cells in a filamentous organization (order Trentepohliales). In contrast to these two groups, the other groups possess multinucleate cells. Representatives of the third group (Cladophorales) are branched filamentous seaweeds consisting of multinucleate cells with a few to thousands of nuclei arranged in non-motile cytoplasmic domains (siphonocladous organization). Members of the fourth group (Bryopsidales) are essentially unicellular: they consist of a single, giant tubular cell with thousands to millions of nuclei and complex patterns of cytoplasmic flow (siphonous organization). This siphonous cell can branch and coalesce to form highly complex seaweeds that dominate the flora of tropical coastal ecosystems (Vroom and Smith 2003). The seaweeds belonging to the fifth group (order Dasycladales) also feature a siphonous organization. Acetabularia and Batophora (Dasycladales) form an exception, because they have a single, giant nucleus situated in the rhizoid with which the alga is attached to its rocky substrate. Before sexual reproduction, this nucleus divides meiotically followed by several mitotic divisions, leading to the formation of numerous nuclei that populate the gametes. In addition to these five major multicellular or multinucleate groups, the Ulvophyceae also include the genus Ignatius, a soil alga forming clusters of a few cells (Watanabe and Nakayama 2007), and Blastophysa, a microscopic endophytic green alga. Several problems surround the classification of the Ulvophyceae. First, the monophyly of the Ulvophyceae has been questioned since its establishment because it lacks unique ultrastructural synapomorphies (Mattox and Stewart 1984, O'Kelly and Floyd 1984, Lewis and McCourt 2004). Second, molecular phylogenetic studies have not fully resolved the relationships among the orders. Most studies did reveal the presence of two major groups: Oltmannsiellopsidales–Ulvales–Ulotrichales, and a clade consisting of Trentepohliales and the siphonocladous and siphonous seaweed orders (Zechman et al. 1990, Watanabe et al. 2001, Lopez- Bautista and Chapman 2003, Watanabe and Nakayama 2007). However, the relationships within the latter clade, and the positions of the enigmatic genera Ignatius and Blastophysa have not been resolved satisfactorily. The Chlorophyta thus offer a unique opportunity to study the proliferation of cytological types, morphological complexity, ecophysiological adaptations and life cycle evolution. A first step towards
22 CHAPTER 2 understanding this diversification is to resolve the phylogenetic relationships among the UTC classes and the ulvophycean orders. The fact that previous molecular phylogenetic analyses have not yielded a satisfactory resolution of these taxa can be attributed at least in part to the difficulty in obtaining a good combination of taxon and gene sampling. Single-gene analyses with good taxon sampling have suffered from poor resolving power due to the low number of characters (Watanabe and Nakayama 2007). Conversely, studies based on longer alignments from complete organelle genomes have suffered from sparse and uneven taxon sampling (Pombert et al. 2004, Pombert et al. 2005), which can lead to systematic error in phylogenetic analysis (Brinkmann et al. 2005, Philippe et al. 2005). Our goal in this study is to infer ancient relationships within the Chlorophyta, more specifically the divergence of UTC classes and ulvophycean orders. Our approach consists of phylogenetic analysis of a dataset that offers a good balance between taxon and gene sampling. Our alignment consists of seven single-copy nuclear markers, SSU nrDNA and two plastid genes for 43 taxa representing the major lineages of the Viridiplantae. Phylogenetic analyses are carried out with model-based techniques, paying careful attention to the selection of suitable partitioning strategies and models of sequence evolution. Noise-reduction techniques targeted at improving signal in the epoch of interest are applied. Figure 1. The three alternative topologies for Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC) have been supported by ultrastructural characteristics, molecular phylogenies and/or genomic structural features. Topology hypothesis testing using an AU tests based on our dataset containing seven nuclear genes, SSU nrDNA and two plastid genes suggested that an alternative branching order for the UTC classses (second column) was not significantly worse than the ML solution (first column), which supports a sister relationship between the Ulvophyceae and Chlorophyceae. Topology hypothesis testing using Bayesian factors provided very strong support in favor of the T(UC) topology. Results We generated EST data from a siphonocladous ulvophyte, Cladophora coelothrix, to facilitate the development of PCR primers for single-copy nuclear genes across the green algae. We selected 43 taxa representing all major lineages of the green algae and obtained DNA sequences for seven nuclear genes, the nuclear SSU rDNA and two plastid genes (Fig. S1, Table S1). The concatenated matrix is 10209 bp long and is 63% filled at the gene level and 61% at the nucleotide level (Fig. S1).
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 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 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
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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
Page 60 and 61: Methods Algal strains GAIN AND LOSS
Page 64 and 65: Authors' contributions GAIN AND LOS
Page 66 and 67: Additional file 2 GAIN AND LOSS OF
Page 68 and 69: Additional file 4 GAIN AND LOSS OF
Page 70 and 71: Additional file 6 Table S2. GenBank
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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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