| Preface | p. v |
| Foreword | p. vii |
| Introduction | p. 1 |
| Comparative Genomics | p. 3 |
| Mechanisms | p. 9 |
| Cytogenetics, Molecular Genetics, Population Genetics | p. 11 |
| Benefits of a Model of Segregation for the Understanding of Chromosomal Evolution | p. 13 |
| Fixation of Chromosomal Rerrangements | p. 19 |
| The Pathological Consequences and Evolutionary Implications of Recent Human Genomic Duplications | p. 29 |
| High Frequency of Inversions During Eukaryote Gene Order Evolution | p. 47 |
| Human and Mouse DNA Sequence Comparisons: Further Evidence for a Mosaic Model of Genomic Evolution | p. 59 |
| Hot Spots in Chromosomal Breakage: From Description to Etiology | p. 71 |
| Organelles: Mitochondria and Chloroplats | p. 85 |
| Rearrangements in Small Genomes | p. 87 |
| Chloroplast Gene Order and the Divergence of Plants and Algae, from the Normalized Number of Induced Breakpoints | p. 89 |
| An Empirical Comparison of Phylogenetic Methods on Chloroplast Gene Order Data in Campanulaceae | p. 99 |
| Gene Order and Phylogenetic Information | p. 123 |
| The Duplication/Random Loss Model for Gene Rearrangement Exemplified by Mitochondrial Genomes of Deuterostome Animals | p. 133 |
| MAPIT--A Semi-Automated Approach to the Representation of Genetic Maps | p. 149 |
| Combinatorial Algorithms | p. 163 |
| A New Set of Problems for a New Kind of Data | p. 165 |
| Experimental and Statistical Analysis of Sorting by Reversals | p. 171 |
| The Syntenic Diameter of the Space of N-Chromosome Genomes | p. 185 |
| Circular Permutations and Genome Shuffling | p. 199 |
| The Complexity of Calculating Exemplar Distances | p. 207 |
| An Alternative Algebraic Formalism for Genome Rearrangements | p. 213 |
| Approximation Algorithms for the Median Problem In the Breakpoint Model | p. 225 |
| Algorithms for Constructing Comparative Maps | p. 243 |
| Prokaryotes | p. 263 |
| Genome Scrambling versus Functional Clustering | p. 265 |
| Dynamics of Gene Order Structures and Genomic Architectures | p. 267 |
| Comparative Genome Analysis: Exploiting the Context of Genes to Infer Evolution and Predict Function | p. 281 |
| Statistics | p. 295 |
| The Quantification of Comparative Mapping | p. 297 |
| Accuracy and Robustness of Analyses Based on Numbers of Genes in Observed Segments | p. 299 |
| Marker Density and Estimates of Chromosome Rearrangement | p. 307 |
| Estimating the Number of Conserved Segments Between Species Using a Chromosome Based Model | p. 321 |
| CHROMTREE: Maximum Likelihood Estimation of Chromosomal Phylogenies | p. 333 |
| Nuclear Genomes | p. 343 |
| Evolutionary Inference from Comparative Mapping | p. 345 |
| Evolution of Karyotype Organisation in Accipitridae: a Translocation Model | p. 347 |
| Syntenies of Unrelated Genes Conserved in Mammals and Nonvertebrates (A Review) | p. 357 |
| Companion Animal Genetics | p. 367 |
| The Essential Role of Comparative Maps in Livestock Genomics | p. 401 |
| Comparative Genetics: From Hexaploid Wheat to Arabidopsis | p. 411 |
| Unraveling Crucifer Genomes Through Comparative Mapping | p. 425 |
| Comparative Genomics of Plant Chromosomes | p. 439 |
| Gene and Genome Duplication and Multi-gene Families | p. 459 |
| How Can Duplication be Analyzed? | p. 461 |
| Recovery of Ancestral Tetraploids | p. 465 |
| Genome Archaeology: Detecting Ancient Polyploidy in Contemporary Genomes | p. 479 |
| Polyploidization and Vertebrate Origins: A Review of the Evidence | p. 493 |
| A Formal Model of Genomic DNA Multiplication and Amplification | p. 503 |
| A Simple Evolutionary Model for Genome Phylogeny Based on Gene Content | p. 515 |
| GeneTree: A Tool for Exploring Gene Family Evolution | p. 525 |
| Duplication, Rearrangement, and Reconciliation | p. 537 |
| Author Index | p. 551 |
| Subject Index | p. 553 |
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