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Introduces the theoretical and controversial aspects of molecular techniques in systematics and evolutionary biology. The first part of this book deals with important applications of evolutionary and systematic analysis at different taxonomic levels. The second part discusses DNA multiple sequence alignment, species designations using molecular data, evo-devo and other topics that are problematic or controversial. In the last part, novel topics in molecular evolution and systematics, like genomics, comparative methods in molecular evolution and the use of large data bases are described.