A comprehensive account of genomic rearrangement, focusing on the mechanisms of inversion, translocation, gene and genome duplication and gene transfer and on the patterns that result from them in comparative maps. Includes analyses of genomic sequences in organelles, prokaryotes and eukaryotes as well as comparative maps of the nuclear genomes in higher plants and animals. The book showcases a variety of algorithmic and statistical approaches to rearrangement and map data.
A comprehensive account of genomic rearrangement, focusing on the mechanisms of inversion, translocation, gene and genome duplication and gene transfer and on the patterns that result from them in comparative maps. Includes analyses of genomic sequences in organelles, prokaryotes and eukaryotes as well as comparative maps of the nuclear genomes in higher plants and animals. The book showcases a variety of algorithmic and statistical approaches to rearrangement and map data.
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.
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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