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

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actin G6PI GapA histone OEE1 40S_S9 60S_L3 60S_L17 Prasinophyceae Chlorodendrales Scherffelia dubia AF061018 DQ270259 AJ919716 AJ919712 AL132935 AJ919390 Tetraselmis spp R76 (T. striata) R76 (T. striata) R76 (T. striata) R76_Oxy2/ AB293977 R76 (T. striata) (T. cordiformis) Mamiellales Ostreococcus tauri CR954216 Steven DQ649076 R68_2 R68 R68 CR954206 Pseudoscourfieldiales Nephroselmis olivacea EC732532 R112_clon R112_2_GapM R112 R112/ AB293978 Streptophyta Mesostigmatales Mesostigma viride AF061020 R111 R111_11 R111 R111/ DN255652 R111 R111 Chlorokybales Chlorokybus atmophyticus R99 DQ270263 R99 Klebsormidiales Entransia fimbriata R101 R101_1_Oxy1 R101 Klebsormidium flaccidum R46_7 R67 R67_1_Oxy2 R67_2 R67 R67 Zygnematales Closterium sp. R4 R4_3 AB293981 R113_3 (C. orbicularis) Spirogyra sp. AF061021 AJ246030 Coleochaetales Coleochaete spp AF061019 (C. scutata) DQ270264 (C. scutata) Charales AB293979 (C. braunii) Chara spp DQ846905 (C. contraria) DQ270262 (C. vulgaris) Embryophyta (land plants) Marchantiophyta (Liverworts) Marchantia polymorpha AB100427 BJ863864 AJ246026 AB185062 BJ844290 BJ861755 BJ852563 BJ853031 Bryophyta (Mosses) Physcomitrella patens XM_001782636 XM_001760154 DQ270266 BJ975811 XM_001763206 XM_001754317 XM_001782386 XM_001767807 Spermatophyta (Seed plants) Arabidopsis thaliana M20016 AB044951 NM_101161 X60429 AJ145957 AB010077 M32655 AC004393 Oryza sativa X16280 D45217 NM_001059519 NM_001056811 NM_001049669 NM_001055539 D12630 NM_001069236 other eukaryotes Archaeplastida Glaucocystophyta Cyanophora paradoxa CPU90325 DQ812897 DQ270258 ES235644 AJ784854 EC666063 EC661414 EC666069 Rhodophyta Cyanidiophyceae Cyanidioschyzon merolae D32140 CMT497C_Steven AP006492 AP006496 AB159597 AP006495
38 CHAPTER 2 Table S1 continued. Genbank accession numbers for nucleotide sequences of atpB, rbcL and SSU rDNA. Chlorophyta Ulvophyceae Ulotrichales Ulvales atpB rbcL SSU rDNA Halochlorococcum moorei AY198122 Acrochaete repens FJ715715 FJ715684 Bolbocoleon piliferum FJ715716 AY205330 Enteromorpha sp. AY422552 AJ000040 Ulva sp. AF499668 (U. fenestrate) Ignatius-clade Ignatius tetrasporus AB110439 Bryopsidales Bryopsis sp. FJ480417 (B. plumosa) FJ715718 FJ715685 (B. plumosa) Codium sp. M67453 (C. fragile) FJ715686 (C. platylobium) Derbesia sp. AF212142 (D. marina) Halimeda spp FJ480416 (H. discoidea) FJ715719 (H. incrassate) AY786526 (H. gracilis) Dasycladales Acetabularia spp FJ480413 (A. dentate) FJ715714 (A. acetabulum) Z33461 (A. acetabulum) Bornetella spp FJ480414 (B. nitida) FJ715717 (B. sphearica) Z33464 (B. nitida) Siphonocladales Boergesenia forbesii AM498746 Boodlea composita AF510157 Cladophora albida Z35317 Cladophora coelothrix Z35315 Phyllodictyon spp AF510163 (P. pulcherrimum) Siphonocladus tropicus AM498761 Valonia utricularis Z35323 Trentepohliales Chlorophyceae Trebouxiophyceae Prasinophyceae Streptophyta Trentepohlia aurea FJ534608/FJ715722 AB110783 Chlamydomonas reinhardtii NC 005353 NC 005353 M32703 Scenedesmus obliquus NC008101 NC008101 X56103 Volvox carteri AB013999 D63446 Chlorella spp NC 001865 (C. vulgaris) NC 001865 (C. vulgaris) X13688 (C. vulgaris) Prototheca wickerhamii AJ245645 X74003 Chlorodendrales Tetraselmis spp DQ173248 (T. chuii suecica) DQ173247 (T. chuii suecica) X70802 (T. striata) Mamiellales Ostreococcus tauri NC 008289 NC 008289 AY329635 Pseudoscourfieldiales Nephroselmis olivacea NC 00927 NC 00927 X74754 Mesostigmatales Mesostigma viride NC 002186 NC 002186 AJ250109 Chlorokybales Chlorokybus atmophyticus DQ422812 DQ422812 M95612 Klebsormidiales Entransia fimbriata AY823688 E88 slordig LB2793 Klebsormidium flaccidum AF408801 E87 rbcL2 X75520 Zygnematales Closterium spp AJ553936 (C. lunula) AF352237 (C. gracile)
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 42 and 43: PHYLOGENY OF GREEN ALGAE 35 Figure
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
Page 100 and 101:
A MULTI-LOCUS TIME-CALIBRATED PHYLO
Page 102 and 103:
Page 104 and 105:
Page 106 and 107:
Time-calibrated phylogeny A MULTI-L
Page 108 and 109:
Page 110 and 111:
Page 112 and 113:
Page 114 and 115:
Acknowledgments A MULTI-LOCUS TIME-
Page 116 and 117:
Dichotomosiphon tuberosus AB038487
Page 118 and 119:
Table 3. List of calibration points
Page 120:
Page 123 and 124:
116 CHAPTER 7 Introduction Green al
Page 125 and 126:
118 CHAPTER 7 ulvophycean order Ulo
Page 127 and 128:
120 CHAPTER 7 10). Filaments that w
Page 129 and 130:
122 CHAPTER 7 invaded freshwater ha
Page 131 and 132:
124 CHAPTER 7 filaments, and the po
Page 133 and 134:
126 CHAPTER 7 Type species: Okellya
Page 136 and 137:
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
Page 144 and 145:
GENERAL DISCUSSION 137 Our site str
Page 146 and 147:
GENERAL DISCUSSION 139 In the light
Page 148:
GENERAL DISCUSSION 141 genomes (Rok
Page 151 and 152:
144 REFERENCES Bartsch I and Kuhlen
Page 153 and 154:
146 REFERENCES Derelle E, Ferraz C,
Page 155 and 156:
148 REFERENCES Hanyuda T, Wakana I,
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150 REFERENCES Knight RD, Freeland
Page 159 and 160:
152 REFERENCES Mattox K and Stewart
Page 161 and 162:
154 REFERENCES Philippe H, Lartillo
Page 163 and 164:
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
Page 169 and 170:
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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