This study focuses on the evolving linear structure of the genome, from organelles and prokaryotes through to the multichromosomal nuclear genomes of plants and animals, based on modern genome map and sequence data. The collection brings together the diverse range of combinatorial optimization and probabilistic modeling techniques for analyzing genome rearrangements in the context of clinical cytogenetics, molecular genetics, population biology, microbial genomics, and the domesticated plant and animal genome projects. It critically compares functional and neutral conceptions of genome rearrangement and represents a concerted attack on the modeling and analytical problems associated with gene and genome duplication and with multigene families.