Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families

Front Matter....Pages i-xiii
Front Matter....Pages 1-1
Comparative Genomics....Pages 3-7
Front Matter....Pages 9-9
Cytogenetics, Molecular Genetics, Population Genetics....Pages 11-12
Benefits of a Model of Segregation for the Understanding of Chromosomal Evolution....Pages 13-18
Fixation of Chromosomal Rerrangements....Pages 19-27
The Pathological Consequences and Evolutionary Implications of Recent Human Genomic Duplications....Pages 29-46
High Frequency of Inversions During Eukaryote Gene Order Evolution....Pages 47-58
Human and Mouse DNA Sequence Comparisons: Further Evidence for a Mosaic Model of Genomic Evolution....Pages 59-69
Hot Spots in Chromosomal Breakage: From Description TC Etiology....Pages 71-83
Front Matter....Pages 85-85
Rearrangements in Small Genomes....Pages 87-88
Chloroplast Gene Order and the Divergence of Plants and Algae, from the Normalized Number of Induced Breakpoints....Pages 89-98
An Empirical Comparison of Phylogenetic Methods on Chloroplast Gene Order Data in Campanulaceae....Pages 99-121
Gene Order and Phylogenetic Information....Pages 123-132
The Duplication/Random Loss Model for Gene Rearrangement Exemplified by Mitochondrial Genomes of Deuterostome Animals....Pages 133-147
MAPIT—a Semi-Automated Approach to the Representation of Genetic Maps....Pages 149-161
Front Matter....Pages 163-163
A New Set of Problems for a New Kind of Data....Pages 165-170
Experimental and Statistical Analysis of Sorting by Reversals....Pages 171-183
The Syntenic Diameter of the Space of N-Chromosome Genomes....Pages 185-197
Circular Permutations and Genome Shuffling....Pages 199-206
The Complexity of Calculating Exemplar Distances....Pages 207-211
An Alternative Algebraic Formalism for Genome Rearrangements....Pages 213-223
Front Matter....Pages 163-163
Approximation Algorithms for the Median Problem in the Breakpoint Model....Pages 225-241
Algorithms for Constructing Comparative Maps....Pages 243-261
Front Matter....Pages 263-263
Genome Scrambling Versus Functional Clustering....Pages 265-266
Dynamics of Gene Order Structures and Genomic Architectures....Pages 267-280
Comparative Genome Analysis: Exploiting the Context of Genes to Infer Evolution and Predict Function....Pages 281-294
Front Matter....Pages 295-295
The Quantification of Comparative Mapping....Pages 297-298
Accuracy and Robustness of Analyses Based on Numbers of Genes in Observed Segments....Pages 299-306
Marker Density and Estimates of Chromosome Rearrangement....Pages 307-319
Estimating the Number of Conserved Segments Between Species Using a Chromosome Based Model....Pages 321-332
Chromtree: Maximum Likelihood Estimation of Chromosomal Phylogenies....Pages 333-342
Front Matter....Pages 343-343
Evolutionary Inference From Comparative Mapping....Pages 345-346
Evolution of Karyotype Organisation in Accipitridae: a Translocation Model....Pages 347-356
Syntenies of Unrelated Genes Conserved in Mammals and Nonvertebrates (A Review)....Pages 357-366
Companion Animal Genetics....Pages 367-399
The Essential Role of Comparative Maps in Livestock Genomics....Pages 401-409
Comparative Genetics: From Hexaploid Wheat to Arabidopsis....Pages 411-423
Unraveling Crucifer Genomes Through Comparative Mapping....Pages 425-437
Comparative Genomics of Plant Chromosomes....Pages 439-457
Front Matter....Pages 459-459
How Can Duplication be Analyzed?....Pages 461-464
Recovery of Ancestral Tetraploids....Pages 465-477
Front Matter....Pages 459-459
Genome Archaeology: Detecting Ancient Polyploidy in Contemporary Genomes....Pages 479-491
Polyploidization and Vertebrate Origins: A Review of the Evidence....Pages 493-502
A Formal Model of Genomic Dna Multiplication and Amplification....Pages 503-513
A Simple Evolutionary Model for Genome Phylogeny Based on Gene Content....Pages 515-523
Genetree: A Tool for Exploring Gene Family Evolution....Pages 525-536
Duplication, Rearrangement, and Reconciliation....Pages 537-550
Back Matter....Pages 551-557