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

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PHYLOGENY OF GREEN ALGAE 35 Figure S3. Phylogeny of the green plant lineage inferred from amino-acid sequences of 7 nuclear genes and plastid genes rbcL and atpB and nucleotide sequences of nuclear SSU rDNA with Bayesian techniques. Numbers at nodes indicate posterior probabilities; values below 0.9 are not shown. Because TreeFinder cannot simultaneously analyze nucleotide and amino acid sequences only MrBayes was used to infer this tree. Amino acid sequences used a WAG model with among-site rate heterogeneity (+ 8), SSU nrDNA was partitioned into loops and stems and used a GTR+ 8 model. Two parallel runs, each consisting of four incrementally heated chains were run for 3 million generations, sampling every thousand generations. Convergence of log-likelihoods and parameter values was assessed in Tracer v1.4 (Rambaut and Drummond 2007). A burnin sample of 300.000 trees was removed before constructing the majority rule consensus tree.
Table S1. Genbank accession numbers for nucleotide sequences of actin, glucose-6-phosphate isomerase, glyceraldehydes-3-phosphate dehydrogenase, histone, oxygen evolving protein, 40S ribosomal protein S9 and 60S ribosomal protein L3 and L17. actin G6PI GapA histone OEE1 40S_S9 60S_L3 60S_L17 Chlorophyta Ulvophyceae Ulotrichales Halochlorococcum moorei R102 R102 R73_2 Ulvales Acrochaete repens R94 R94_Gap2 R94_2 R94 R94_2 Bolbocoleon piliferum R95 R95_GapM R60_2 Enteromorpha sp. R109 R106 R109_GapM R109_1 R109_1_Oxy1 R109_3UTR Ulva sp. AB106563 (U. pertusa) R110_10 R49_2 R110_1 R110_Oxy2 Ignatius-clade Ignatius tetrasporus R66_GapM R66_4 R66 R66 R105 Bryopsidales Blastophysa rhizopus R104 R104_GapM R104 R104 Bryopsis sp. R105 R105_1 R105/ AB293980 (B. plumosa) Codium sp. R63 R63 R63_1_Oxy1 R63 Derbesia sp. R98 R98_2 R98 R98 Halimeda spp KZN2K4_20 (H. cuneata2) R65_1 Dasycladales Acetabularia acetabulum R7 AAL00001487 (TBestDB) R103 R103_1_Oxy2 EC096877 CF259099 Bornetella sphaerica R80 R80_1 R80 Siphonocladales Boergesenia forbesii R21_1 R21_2 R78 R78_1 R78 Boodlea composita R8_1 R38_6 R79_GapM R79 R79_1 R79 Cladophora albida R88_2 R88_19 R88 R88 Cladophora coelothrix R35_3 R35_12 cDNA_lib117 cDNA_lib122 cDNA_lib128 cDNA_lib44 cDNA_lib80 Phyllodictyon spp R18 R85 R85 R85 R85_2 R85 R85 Siphonocladus tropicus R29_3 R84 R84_5 R84 R84_1 R84 Valonia utricularis R86 R86_5 R86 R86 Trentepohliales Trentepohlia aurea R107 R107_Oxy2 Chlorophyceae Chlamydomonas reinhardtii D50838 R44_2 L27668 R96_5 X13826 R96_2 = RPS9 R96 = RPL3 XM_001693402 Scenedesmus obliquus R69 SOL00005809 (TBestDB) R69 R69 EC189050 EC189501 R69 Volvox carteri M33963 X06963 AF110780 FD918100 FD837306 Trebouxiophyceae Chlorella kessleri R97 R97_5 R97_5 R97 R97 R97_1 Helicosporidium sp. AF317896 CX128748 CX128902 CX128917 Prototheca wickerhamii EC181529 EC181191 EC183246 EC180670
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 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 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
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
Page 72 and 73: atpB rbcL SSU rDNA EF-1α EFL Chlor
Page 74 and 75: atpB rbcL SSU rDNA EF-1α EFL choan
Page 76 and 77: 4 Complex phylogenetic distribution
Page 78 and 79: NON-CANONICAL GENENTIC CODE 71 addi
Page 80 and 81: Figure 1. The occurrence of a non-c
Page 82 and 83: NON-CANONICAL GENENTIC CODE 75 Figu
Page 84 and 85: Multiple independent gains NON-CANO
Page 86: Acknowledgements NON-CANONICAL GENE
Page 89 and 90: 82 CHAPTER 5 Introduction The genet
Page 91 and 92: 84 CHAPTER 5 The goal of this study
Page 93 and 94:
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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Page 104 and 105:
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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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Page 123 and 124:
116 CHAPTER 7 Introduction Green al
Page 125 and 126:
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
Page 153 and 154:
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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