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

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Additional files PHYLOGENY OF GREEN ALGAE 33 Figure S2. Phylogeny of the green plant lineage obtained by maximum likelihood inference of the complete dataset containing 7 nuclear genes, nuclear SSU rDNA and plastid genes rbcL and atpB. Numbers at nodes indicate ML bootstrap values (top) and posterior probabilities (bottom); values below respectively 50 and 0.9 are not shown.
ibosomal RNA plastid genes ribosomal protein-coding genes other nuclear genes nuclear SSU rDNA (18S) atpB rbcL 40S S9 60S L3 60S L17 actin G6PI GapA OEE1 1974 bp 1380 bp 1380 bp 537 bp 1152 bp 468 bp 1122 bp 753 bp 966 bp 477 bp Cyanophora paradoxa 1953 1380 1380 520 1152 468 1122 753 966 477 99% of sites Cyanidioschyzon merolae 1974 1380 633 1122 753 723 477 62% of sites Mesostigma viride 1953 1380 1380 1141 424 1122 684 966 453 92% of sites Chlorokybus atmophyticus 1971 1380 1380 741 966 63% of sites Klebsormidium flaccidum 1953 1254 658 537 1137 424 966 428 63% of sites Entransia fimbriata 1936 1254 1316 1140 451 57% of sites Coleochaete sp. 1953 1255 1354 1122 963 63% of sites Spirogyra sp. 1254 1372 1110 966 45% of sites Closterium sp. 1974 1353 1060 753 474 54% of sites Chara sp. 1940 1254 1380 900 966 477 64% of sites Marchantia polymorpha 1953 1380 1380 537 1068 468 648 753 966 477 89% of sites Physcomitrella patens 1974 1380 1310 537 1152 468 1122 753 966 477 99% of sites Oryza sativa 1974 1380 1380 537 1152 468 1122 753 966 477 100% of sites Arabidopsis thaliana 1971 1380 1380 537 1152 468 1122 753 966 477 100% of sites Ostreococcus tauri 1973 1380 1380 1134 468 1011 753 966 453 92% of sites Nephroselmis olivacea 1974 1380 1380 412 657 519 441 54% of sites Scherffelia dubia 242 1059 465 1122 966 264 34% of sites Tetraselmis sp. 1953 1266 1356 424 883 738 418 64% of sites Chlorella sp. 1953 1380 1380 424 900 753 966 428 77% of sites Prototheca wickerhamii 1974 1380 373 1101 468 1118 61% of sites Helicosporidium 399 468 893 14% of sites Scenedesmus obliquus 1953 1380 1380 537 1120 424 833 507 420 77% of sites Chlamydomonas reinhardtii 1974 1380 1380 537 1152 468 1122 753 966 477 100% of sites Volvox carteri 1227 1350 537 1152 1122 477 56% of sites Halochlorococcum 1960 891 742 33% of sites Bolbocoleon piliferum 1922 613 687 519 24% of sites Acrochaete repens 1928 1325 537 753 520 426 48% of sites Ulva intestinalis 1971 1353 537 870 744 513 451 56% of sites Ulva sp. 1563 1354 1122 753 966 417 56% of sites Ignatius tetrasporus 1954 424 519 441 27% of sites Trentepohlia aurea 1961 1167 417 32% of sites Acetabularia sp. 1973 1142 1320 551 130 949 753 428 57% of sites Bornetella sp. 1973 1141 1318 906 435 53% of sites Halimeda sp. 1949 1209 1326 753 49% of sites Derbesia sp. 1323 714 966 435 32% of sites Bryopsis sp. 716 1197 1323 1083 900 442 39% of sites Codium sp. 729 1380 424 955 452 26% of sites Blastophysa rhizopus 741 519 428 12% of sites Cladophora albida 1972 424 714 906 38% of sites Valonia utricularis 1889 424 753 440 33% of sites Phyllodictyon sp. 1889 537 1149 424 831 753 438 55% of sites Boodlea composita 1889 537 424 900 753 519 453 46% of sites Cladophora coelothrix 1889 537 1152 468 900 753 477 58% of sites Boergesenia forbesii 1927 537 424 900 753 41% of sites Siphonocladus tropicus 1927 537 424 900 753 441 45% of sites 78% of sites 50% of sites 61% of sites 37% of sites 36% of sites 47% of sites 49% of sites 65% of sites 48% of sites 67% of sites Fig. S1. Data availability matrix. Graphical representation of our concatenated alignment, showing the availability of sequence data. The color of column and row headers indicate the amount of data available for that column or row. Green indicates high data availability, red indicates low data availability and yellow/orange represents intermediate data availability. outgroup Streptophyta Prasinophyceae Trebouxiophyceae Chlorophyceae Ulvophyceae 0% 20% 40% 60% 80% 100% Data availability: percent of sites present
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 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
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
Page 95 and 96:
88 CHAPTER 5 Codon usage bias and G
Page 98 and 99:
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:
Page 106 and 107:
Time-calibrated phylogeny A MULTI-L
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Page 110 and 111:
Page 112 and 113:
Page 114 and 115:
Acknowledgments A MULTI-LOCUS TIME-
Page 116 and 117:
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
Page 129 and 130:
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
Page 138 and 139:
SSU nrDNA phylogenies GENERAL DISCU
Page 140 and 141:
GENERAL DISCUSSION 133 copy nuclear
Page 142 and 143:
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.
Page 165 and 166:
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
Page 172 and 173:
Samenvatting Groenwieren worden wer
Page 174 and 175:
SAMENVATTING 167 kleine variaties o
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