Part I: Self/Nonself Evolution, ​A new view of how MHC class I molecules fight disease: generalists and specialists.- Evolution and diversity of defensins in vertebrates.- Interdependencies between the adaptation and interference modules guide efficient CRISPR-Cas immunity.- How the other half lives: CRISPR-Cas's influence on bacteriophages.- Hidden Silent Codes in Viral Genomes.- Self and Non-Self from a Genomic Perspective: Transposable Elements.- Mammalian-specific traits generated by LTR retrotransposon-derived SIRH genes.- Part II: Species Evolution and Evolution of Complex Traits, The life history of domesticated genes illuminates the evolution of novel mammalian genes.- Evolution of Complex Traits in Human Populations.- The descent of bison.- Convergent and parallel evolution in early Glires (Mammalia).- Reductive evolution of apicomplexan parasites from phototrophic an-cestors.- Part III: Methods and Concepts, Evolution of milk oligosaccharides and their function in monotremes and marsupials.- Mechanistic Models of Protein Evolution.- Genome-wide screens for molecular convergent evolution in mammals.- Assessing evolutionary potential in tree species through ecology-informed genome screening.- Evolutionary constraints on coding sequences at the nucleotidic level: a statistical physics approach.- Case studies of seven gene families with unusual high retention rate since the Vertebrate and Teleost Whole Genome Duplications.