chapter 1 An overview on eukaryote origins and evolution: the beauty of the cell and the fabulous gene phylogenies -- chapter 2 Excavata and the origin of amitochondriate eukaryotes -- chapter 3 The evolutionary history of plastids: a molecular phylogenetic perspective -- chapter 4 Chromalveolate diversity and cell megaevolution: interplay of membranes, genomes and cytoskeleton -- chapter 5 Origin and Evolution of animals, fungi and their unicellular allies (Opisthokonta) -- chapter 6 Pitfalls in tree reconstruction and the phylogeny of eukaryotes -- chapter 7 The importance of evolutionary biology to the analysis of genome data -- chapter 8 Eukaryotic phylogeny in the age of genomics: evolutionary implications of functional differences -- chapter 9 Genome phylogenies -- chapter 10 Genomics of microbial parasites: the microsporidial paradigm -- chapter 11 Evolutionary contribution of plastid genes to plant nuclear genomes and its effects on the composition of the proteomes of all cellular compartments -- chapter 12 Protein translocation machinery in chloroplasts and mitochondria: structure, function and evolution -- chapter 13 Mitosomes, hydrogenosomes and mitochondria; variations on a theme? -- chapter 14 Eukaryotic cell evolution from a comparative genomic perspective: the endomembrane system -- chapter 15 The membranome and membrane heredity in development and evolution -- chapter 16 Epigenetic inheritance and evolutionary adaptation.