Abstract 133 6.1 Introduction 134 6.2 Pitfalls in Tree Reconstruction Methodologies 135

6.2.2 Compositional Biases 136 6.2.3 Long-Branch Attraction 137 6.2.4 Heterotachy 139 6.2.5 Rare Genomic Events as an Alternative Approach? 139

6.3 LGTs and the Quest for a Species Phylogeny 142 6.4 Toward a Resolution of the Eukaryotic Phylogeny? 144

6.4.1 The Archezoa Hypothesis 144 6.4.2 Single-Gene Approaches 144 6.4.3 Multigene Approaches 145

6.5 Perspective 146 Acknowledgment 146 References 146

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. This chapter describes the principally encountered artifacts, notably long-branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as used for standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g., (1) the bacterial rooting of the universal tree of life, (2) the early emergence of

amitochondriate lineages in eukaryotic phylogenies; and (3) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient datasets and from novel analyses of large combination of genes.