Table of Contents
I. Eutherian Phylogeny and Protein Evolution.- 1 Information for Molecular Studies from Anatomical and Fossil Evidence on Higher Eutherian Phylogeny.- 1. Introduction.- 2. A Historical Sketch.- 3. Eutherian Monophyly.- 4. Higher Level Eutherian Phylogeny.- 4.1. Edentata, Pholidota.- 4.2. Carnivora, Creodonta.- 4.3. Rodentia, Lagomorpha, Macroscelidea.- 4.4. “Archontans” and Insectivora.- 4.5. The Ungulate Radiation: Perissodactyla, Artiodactyla, Cetacea, Proboscidea, Tubulidentata, Hyracoidea, Sirenia.- 5. Divergence Times for Eutherian Orders.- 6. Eutherian Phylogeny, Fossil History, and Evolutionary Rates.- References.- 2 Evolution of Mammalian Pancreatic Ribonucleases.- 1. Introduction.- 2. Trees.- 2.1. Most Parsimonious Tree.- 2.2. Biologic Tree.- 3. Evolutionary Rates.- 4. Three-Dimensional Structure of Ribonuclease.- 5. Enzymic Activity on Low-Molecular-Weight Nucleotide Substrates and on RNA.- 6. Enzymic Activity on Double-Stranded RNA.- 7. Interaction with Inhibitor Proteins.- 8. Glycosylation and the Function of Carbohydrate.- References.- 3 Eye Lens Proteins and Vertebrate Phylogeny.- 1. Introduction.- 2. Comparative Anatomy and Evolution of the Lens.- 3. Comparative Studies of Lens Proteins.- 3.1. The Crystallins.- 3.2. Intraspecies Variation in Lens Proteins.- 3.3 Crystallin Variation between Species.- 4. Structural Analysis of ?-Crystallin.- 4.1. Isolation of ?-Crystallin.- 4.2. Electrophoresis of the ?-Crystallin Chains.- 4.3. Sequence Analysis of ?A Chains.- 4.4. Phylogenetic Reconstructions.- 5. Phylogenetic Inferences from ?-Crystallin A Sequences.- 5.1. Mammalian Phylogeny.- 5.2. Relationships among Vertebrate Classes and Subclasses.- 6. Molecular Aspects of ?-Crystallin Evolution.- 6.1. Parallel and Back Substitutions.- 6.2. Changes in Charge Are Avoided.- 6.3. “Covarions”.- 6.4. Variable Rates of Change and a Directional Trend in Substitutions.- 6.5. Unequal Distribution of Substitutions over the ?A Chain.- References.- 4 Amino Acid Sequence Evidence on the Phylogeny of Primates and Other Eutherians.- 1. Introduction.- 2. Genealogic Evidence from Amino Acid Sequences.- 2.1. Tree Construction Strategy.- 2.2. Sequences Analyzed.- 2.3. Gnathostome Myoglobin Genealogy.- 2.4. Genealogic Evidence from Other Gene Phylogenies.- 2.5. Species Phylogeny from Combined Sequence Data.- 3. Utilizing the Clock Model of Protein Evolution.- 3.1. Rationale and Procedure.- 3.2. Results Obtained by the Clock Model.- 4. The Tempo and Mode of Protein Evolution.- 4.1. Pattern of Rate Variations.- 4.2. The Central Role of Natural Selection.- 5. Conclusions.- Epilogue: New Cladistic Findings on Globin Phylogeny.- References.- 5 Evolution of Chromosomal Proteins.- 1. Introduction.- 2. Nucleosome Structure.- 2.1. The Chromatin Fiber.- 2.2. The Nucleosome and Nucleosome Core.- 3. Computer Methods.- 3.1. Detection of Protein Relationships.- 3.2. Protein Alignments and Evolutionary Trees.- 3.3. Protein Families and Superfamilies.- 3.4. Mutation Acceptance Rates.- 4. Chromosomal Proteins.- 4.1. Prokaryote DN?-Binding Proteins.- 4.2. Viral Nucleic Acid-Binding Proteins.- 4.3. Protamines.- 4.4. Nonhistone Chromosomal Proteins.- 4.5. Histones H1 and H5.- 4.6. Histone H2A and Nuclear Protein A24.- 4.7. Histone H2B.- 4.8. Histone H3.- 4.9. Histone H4.- 4.10. Mutation Acceptance Rates.- 4.11. The Core Histone Superfamily.- References.- II. Modeling the Process of Sequence Divergence.- 6 Simulation of the Evolution of Macromolecular Sequences by Random Fixation of Allowed Codons.- 1. Introduction.- 2. The Simulation Model—RFAC.- 2.1. The Input Data.- 2.2. The Starting DNA Sequence.- 2.3. Random Point Mutation.- 2.4. Allowed Amino Acids.- 2.5. Fixation.- 2.6. Phylogenies.- 3. Comparison of RFAC with Other Models.- 4. Methods of Comparison of Macromolecular Sequence Divergence in Real and Simulated Evolution.- 5. Results.- 5.1. Effects of Rate of Fixation and Amount of Allowed Variation on Macromolecular Sequence Divergence.- 5.2. Fitting of Simulated to Real Results of Evolution.- 5.3. Effect of Amount of Allowed Variation on “Efficiency” of Evolution.- 6. Conclusions and Discussion.- References.- 7 Nonuniform Molecular Divergence: The Quantitative Evolutionary Analysis of Genes and Messenger RNAs under Selective Structural Constraints.- 1. Introduction.- 2. Constrained Stochastic Theory.- 3. Magnitude of Selective Constraints.- 3.1. Base Composition.- 3.2. Base Replacement Probabilities.- 3.3. Density of Fixed Mutations among Variable Codons.- 3.4. Distribution of Fixed Mutations within Codons.- 4. Estimation of Parameters.- 4.1. The Observational Principle Underlying Parameter Estimation in Gene Sequences.- 4.2. Evolutionary Measures.- 5. A Comparison of Evolutionary Estimates Made from Protein and Nucleic Acid Sequence Data and from Nonrandom REH Theory.- 5.1. A Closely Related Divergence: Mouse and Rabbit ?-Hemoglobin.- 5.2. A Distantly Related Divergence: Rabbit ?- and ?-Hemoglobin.- 6. Comparison of Calculation with Experiment.- 7. Generality of Results.- 8. Extension to Noncoding Regions.- 9. Importance of Accurate Genetic Distance Estimates to Systematics.- 10. Discussion.- 11. Conclusions.- References.- III. Prospects for Investigating Evolution through Genomic DNA.- 8 Genomic DNA: New Approaches to Evolutionary Problems.- 1. Introduction.- 2. Overview of Methods.- 3. Comparative Studies of Genomic DNA.- 3.1. Y-Chromosome DNA.- 3.2. Other Middle-Order Reiterated DNAs.- 3.3. Studies of the Ribosomal Genes.- 3.4. Studies of Single-Copy DNA.- 3.5. DNA Polymorphisms.- 3.6. Other DNAs.- 4. Conclusions.- References.- 9 Features of Gene Structure, Organization, and Expression That Are Providing Unique Insights into Molecular Evolution and Systematics.- 1. Introduction.- 2. Recombinant DNA Technology.- 2.1. Cloning.- 2.2. DNA and RNA Sequencing.- 3. Expression and Organization of Eukaryotic Genes.- 3.1. DNA Transcription and Processing of RNA.- 3.2. The Intervening Sequences of Genes.- 3.3. The Role of Intervening Sequences.- 3.4. Gene Duplication.- 3.5. Pseudogenes.- 4. Use of Nucleotide Sequences in Evolutionary Tree-Building.- 4.1. Why Nucleotide Sequences?.- 4.2. Tree-Building Strategy.- 4.3. A Hemoglobin Nucleotide Tree.- 5. Concluding Remarks.- References.
