Description: Comparative Genomics.- 1. Mechanisms.- Cytogenetics, Molecular Genetics, Population Genetics.- Benefits of a Model of Segregation for the Understanding of Chromosomal Evolution.- Fixation of Chromosomal Rerrangements.- The Pathological Consequences and Evolutionary Implications of Recent Human Genomic Duplications.- High Frequency of Inversions During Eukaryote Gene Order Evolution.- Human and Mouse DNA Sequence Comparisons: Further Evidence for a Mosaic Model of Genomic Evolution.- Hot Spots in Chromosomal Breakage: From Description to Etiology.- 2. Organelles: Mitochondria and Chloroplats.- Rearrangements in Small Genomes.- Chloroplast Gene Order and the Divergence of Plants and Algae, from the Normalized Number of Induced Breakpoints.- An Empirical Comparison of Phylogenetic Methods on Chloroplast Gene Order Data in Campanulaceae.- Gene Order and Phylogenetic Information.- The Duplication/Random Loss Model for Gene Rearrangement Exemplified by Mitochondrial Genomes of Deuterostome Animals.- MAPIT--A Semi-Automated Approach to the Representation of Genetic Maps.- 3. Combinatorial Algorithms.- A New Set of Problems for a New Kind of Data.- Experimental and Statistical Analysis of Sorting by Reversals.- The Syntenic Diameter of the Space of N-Chromosome Genomes.- Circular Permutations and Genome Shuffling.- The Complexity of Calculating Exemplar Distances.- An Alternative Algebraic Formalism for Genome Rearrangements.- Approximation Algorithms for the Median Problem In the Breakpoint Model.- Algorithms for Constructing Comparative Maps.- 4. Prokaryotes.- Genome Scrambling versus- Functional Clustering.- Dynamics of Gene Order Structures and Genomic Architectures.- Comparative Genome Analysis: Exploiting the Context of Genes to Infer Evolution and Predict Function.- 5.Statistics.- The Quantification of Comparative Mapping.- Accuracy and Robustness of Analyses Based on Numbers of Genes in Observed Segments.- Marker Density and Estimates of Chromosome Rearrangement.- Estimating the Number of Conserved Segments Between Species Using a Chromosome Based Model.- CHROMTREE: Maximum Likelihood Estimation of Chromosomal Phylogenies.- 6. Nuclear Genomes.- Evolutionary Inference from Comparative Mapping.- Evolution of Karyotype Organisation in Accipitridae: a Translocation Model.- Syntenies of Unrelated Genes Conserved in Mammals and Nonvertebrates (A Review).- Companion Animal Genetics.- The Essential Role of Comparative Maps in Livestock Genomics.- Comparative Genetics: From Hexaploid Wheat to Arabidopsis.- Unraveling Crucifer Genomes Through Comparative Mapping.- Comparative Genomics of Plant Chromosomes.- 7. Gene and Genome Duplication and Multi-gene Families.- How Can Duplication be Analyzed?.- Recovery of Ancestral Tetraploids.- Genome Archaeology: Detecting Ancient Polyploidy in Contemporary Genomes.- Polyploidization and Vertebrate Origins: A Review of the Evidence.- A Formal Model of Genomic DNA Multiplication and Amplification.- A Simple Evolutionary Model for Genome Phylogeny Based on Gene Content.- GENETREE: A Tool for Exploring Gene Family Evolution.- Duplication, Rearrangement, and Reconciliation.- Author Index.

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