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

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Topological hypothesis testing PHYLOGENY OF GREEN ALGAE 31 Approximately unbiased tests (AU test, Shimodaira 2002) were used to test the alternative relationships between UTC classes. Site likelihoods were calculated by maximum likelihood optimization in Treefinder using the same model specifications as for phylogenetic inference. AU tests were performed with CONSEL V0.1i (Shimodaira and Hasegawa 2001). In addition Bayes Factors were used to evaluate the alternative branching order between UTC classes (Kass and Raftery 1995). Two additional Bayesian analyses using identical conditions as the original analysis that yielded the T(UC) phylogeny were run while constraining the topology to conform to either C(UT) or U(TC). The harmonic mean estimates of the marginal likelihoods of the competing hypotheses were obtained with the sump command in MrBayes and used to calculate the Bayes Factors (BF) as twice the difference in marginal likelihood between the competing hypotheses (Nylander et al. 2004). Removal of fast-evolving sites: site stripping We applied a modified site stripping approach (Waddell et al. 1999) to improve the signal to noise ratio in the epoch of interest. Site-specific rates were calculated in HyPhy (Pond et al. 2005). Progressive removal of the fastest sites, 5% each time, resulted in a set of alignments that were subjected to ML analysis as described above. We used a novel modus operandi to reveal the trend of signal change with increasing amounts of site stripping and select an optimal site stripping condition (Fig. 3). First, we performed rate smoothing on the ML tree obtained from the complete alignment to make branch lengths roughly proportional to evolutionary time (Fig. 3A), using the nonparametric rate smoothing (NPRS) method with the Powell optimization algorithm implemented in r8s (Sanderson 2003). Second, the epoch of interest (containing the UTC and ulvophycean diversification) was located in the tree. Third, the strength of phylogenetic signal, measured as average bootstrap values (BV) in a sliding window across the rate-smoothed tree, was plotted for all site-stripping conditions (e.g. Fig. 3B). Fourth, we calculated signal gain in the epoch of interest (GE) by integrating the function representing the difference between the BV of the site-stripped condition and the BV of the analysis on the complete alignment across the epoch of interest (Fig. 3C). Finally, these gain values were compared between site stripping conditions, leading to the conclusion that moderate site stripping (25% of characters removed) yielded maximum signal in the epoch of interest (Fig. 3D). The rationale of using BV as a proxy of signal strength is that these values reflect the clarity of the signal in the data, i.e., are inversely related to the amount of conflict in the data (Felsenstein 1985, Soltis and Soltis 2003). It may seem as circular reasoning to use BV to decide on the most suitable site stripping condition and subsequently use BV to come to conclusions about the strength of relationships. However, this is not entirely true because GE is calculated over a wide temporal range and across all lineages in the relevant epoch, so it does not rely exclusively on the BV of the branches we wish to resolve.
32 CHAPTER 2 Acknowledgements We thank Barbara Rinkel, Hervé Moreau, Tatiana Klotchkova, Wytze Stam and Jeanine Olsen for providing cultures, Caroline Vlaeminck for assisting with the molecular work, Klaus Valentin for cDNA library services, Steven Robbens and Yves Van de Peer for early access to Ostreococcus data, Rick Zechman for atpB sequences, Peter Dawyndt for additional processing power, and Wim Gillis for IT support. Funding was provided by the Special Research Fund (Ghent University, DOZA-01107605) and the Research Foundation Flanders (postdoctoral fellowships to HV, FL and ODC). Phylogenetic analyses were largely carried out on the KERMIT computing cluster (Ghent University).
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 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
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
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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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