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

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Contents Chapter 1 General introduction and thesis outline 1 Chapter 2 Ancient relationships among green algae inferred from nuclear and chloroplast genes Chapter 3 Gain and loss of elongation factor genes in green algae 43 Chapter 4 Complex phylogenetic distribution of a non-canonical genetic code in green algae Chapter 5 Codon usage bias and GC content in green algae 81 Chapter 6 A multi-locus time-calibrated phylogeny of the siphonous green algae 91 Chapter 7 Systematics of the marine microfilamentous green algae Uronema curvatum and Urospora microscopica (Chlorophyta) Chapter 8 General discussion 129 References 143 Summary 161 Samenvatting 165 19 69 115
Page 1 and 2: Phylogeny and molecular evolution o
Page 3 and 4: Promotor: Prof. Dr. O. De Clerck (U
Page 5: Aan de mensen van de plantkunde in
Page 9 and 10: 2 CHAPTER 1 Archaeplastida The mono
Page 11 and 12: 4 CHAPTER 1 inconclusive from which
Page 13 and 14: 6 CHAPTER 1 Chlorophyta The current
Page 15 and 16: 8 CHAPTER 1 smallest nuclear genome
Page 17 and 18: 10 CHAPTER 1 Green algal phylogenie
Page 19 and 20: 12 CHAPTER 1 Designing primers for
Page 21 and 22: 14 CHAPTER 1 Missing data Deep phyl
Page 23 and 24: 16 CHAPTER 1 Treefinder). In the se
Page 25 and 26: 18 CHAPTER 1 In Chapter 7 the phylo
Page 27 and 28: 20 CHAPTER 2 Introduction The green
Page 29 and 30: 22 CHAPTER 2 understanding this div
Page 31 and 32: 24 CHAPTER 2 the UTC clades and the
Page 33 and 34: 26 CHAPTER 2 relationships among th
Page 35 and 36: 28 CHAPTER 2 Progress and perspecti
Page 37 and 38: 30 CHAPTER 2 Model selection proced
Page 39 and 40: 32 CHAPTER 2 Acknowledgements We th
Page 41 and 42: ibosomal RNA plastid genes ribosoma
Page 43 and 44: Table S1. Genbank accession numbers
Page 45 and 46: 38 CHAPTER 2 Table S1 continued. Ge
Page 47 and 48: 40 CHAPTER 2 Table S2. Algal strain
Page 49 and 50: 42 CHAPTER 2 Table S4. PCR conditio
Page 51 and 52: 44 CHAPTER 3 Background Elongation
Page 53 and 54: 46 CHAPTER 3 the order Ulvales poss
Page 55 and 56: 48 CHAPTER 3 Figure 2B, the complet
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50 CHAPTER 3 From these results, it
Page 59 and 60:
52 CHAPTER 3 occurred because the d
Page 61 and 62:
54 CHAPTER 3 Cloning and sequencing
Page 63 and 64:
56 CHAPTER 3 where (0,0) indicates
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58 CHAPTER 3 Additional files Addit
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60 CHAPTER 3 Additional file 3
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62 CHAPTER 3 Additional file 5 Tabl
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atpB rbcL SSU rDNA EF-1α EFL Ernod
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atpB rbcL SSU rDNA EF-1α EFL Cyani
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68 CHAPTER 3 Additional file 7 Nexu
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70 CHAPTER 4 Introduction The genet
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72 CHAPTER 4 2009). The output from
Page 81 and 82:
74 CHAPTER 4 If both the phylogeny
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76 CHAPTER 4 Phylogenetic uncertain
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78 CHAPTER 4 in Ulvophyceae as foll
Page 88 and 89:
5 Codon usage bias and GC content i
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CODON USAGE BIAS AN GC CONTENT 83 i
Page 92 and 93:
Results and discussion CODON USAGE
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Growth rate and generation time COD
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CODON USAGE BIAS AN GC CONTENT 89 t
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92 CHAPTER 6 Introduction The sipho
Page 101 and 102:
94 CHAPTER 6 Materials and methods
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96 CHAPTER 6 Phylogenetic analyses
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98 CHAPTER 6 Fig 3. Phylogenetic re
Page 107 and 108:
100 CHAPTER 6 The origin of the ord
Page 109 and 110:
102 CHAPTER 6 Dasycladalean diversi
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104 CHAPTER 6 strata has been assig
Page 113 and 114:
106 CHAPTER 6 One advantage of usin
Page 115 and 116:
108 CHAPTER 6 Table 1. Taxon list w
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110 CHAPTER 6 Table 2. Selection of
Page 119 and 120:
112 CHAPTER 6 Appendix Alternative
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7 Systematics of the marine microfi
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SYSTEMATICS OF MARINE MICROFILAMENT
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Page 128 and 129:
Page 130 and 131:
Page 132 and 133:
Page 134:
Supplementary material SYSTEMATICS
Page 137 and 138:
130 CHAPTER 8 the Chlorophyta has r
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132 CHAPTER 8 chloroplast genes of
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134 CHAPTER 8 recently, often withi
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136 CHAPTER 8 order of the UTC clas
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138 CHAPTER 8 Figure 4. Chronogram
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140 CHAPTER 8 code is found in Dasy
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References Abascal F, Zardoya R, an
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Castresana J. 2000. Selection of co
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REFERENCES 147 Friedl T and O'Kelly
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REFERENCES 149 angiosperms and iden
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REFERENCES 151 Levring T. 1937. Zur
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REFERENCES 153 O'Kelly CJ and Floyd
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REFERENCES 155 Rindi F, López-Baut
Page 164 and 165:
REFERENCES 157 Sogin ML, Elwood HJ,
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REFERENCES 159 Wan XF, Zhou J, and
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Summary Green algae are distributed
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SUMMARY 163 translated to glutamine
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166 SAMENVATTING omvat. Binnen deze
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168 SAMENVATTING In hoofdstukken 6
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