Molecular evolutionary genetics.

This volume in the Monographs in Evolutionary Biology series addresses issues that are part of an emerging area of research loosely called "mo­ lecular evolution. " Its practitioners include both molecular biologists cu­ rious about the evolutionary implications of their data and evolutionary biologists pushing their analyses to the molecular level. The union of these fields of molecular and organismal biology has been turbulent at times, and, as shall be seen, this dialectic has led to some very serious challenges to long-held notions about the role of natural selection in evolution and the economy of genome organization in eukaryotes. As an inevitable outgrowth of molecular biology, molecular evolution is necessarily a young discipline, but it can already point proudly to two major discoveries. The first, is the molecular clock, a concept that has emerged from the analysis of at least four data sets-amino acid sequences, immunologic data, DNA renaturation studies, and, recently, analyses of DNA sequences. The reality of a strong stochastic component in the evolution of nucleotide sequences can no longer be doubted, although the accuracy of the clock with regard to particular sequences and within particular groups of or­ ganisms should be independently measured each time it is used. Never­ theless, molecular clocks will assume increasingly important roles in phy­ logenetic reconstructions, especially since the fossil record is so fragmentary. The second major discovery of molecular evolution has been the incredible complexity of the eukaryotic genome.

1 Evolution of DNA Sequences.- 1. Introduction.- 2. Methods for Estimating the Number of Nucleotide Substitutions between Sequences.- 2.1. Methods.- 2.2. Comparison of Methods.- 3. Rates of Nucleotide Substitution in Various Regions of Genes.- 3.1. Coding Regions.- 3.2. Noncoding Regions.- 3.3. Pseudogenes.- 4. Molecular Clock.- 4.1. The Controversy.- 4.2. A Reevaluation.- 4.3. Rates of Nucleotide Substitution following Gene Duplication.- 5. Patterns of Nucleotide Substitution in Pseudogenes and Functional Genes.- 6. Nonrandom Usage of Synonymous Codons.- 6.1. Patterns of Codon Usage.- 6.2. Factors Affecting Usage of Synonymous Codons.- 7. Concerted Evolution of Multigene Families.- 7.1. Mechanisms of Concerted Evolution.- 7.2. Factors Affecting the Rate of Concerted Evolution.- 7.3. Evolutionary Implications.- 8. Mechanisms of DNA Evolution.- 9. Concluding Remarks.- References.- 2 The Mitochondrial Genome of Animals.- 1. Introduction.- 2. Structure, Content, and Function in Animal Mitochondrial DNA.- 2.1. Gene Content.- 2.2. Genome Structure.- 2.3. Gene Order.- 2.4. Genome Size.- 2.5. Control Region.- 2.6. Replication.- 2.7. Transcription.- 2.8. Strand Distribution of Genes and Nucleotides.- 2.9. Genetic Code and Codon Usage.- 3. Sequence Variation in Animal Mitochondrial DNA.- 3.1. Protein Genes.- 3.2. Transfer RNA Genes.- 3.3. Ribosomal RNA Genes.- 3.4. Other Regions.- 4. Rates of Change in Animal Mitochondrial DNA.- 4.1. Rates of Nucleotide Substitution.- 4.2. Additions and Deletions.- 4.3. Rates of Genome Rearrangements.- 5. Speculations, Problems, and Prospects.- References.- 3 Evolution of Chloroplast and Mitochondrial DNA in Plants and Algae.- 1. Introduction.- 2. Chloroplast Genome Evolution.- 2.1. Chloroplast DNA Inheritance.- 2.2. Cytological Organization of Chloroplast DNA.- 2.3. Physicochemical Properties of Chloroplast DNA.- 2.4. Molecular Organization and Rearrangement of Chloroplast DNA.- 3. Chloroplast Gene Evolution.- 3.1. Evolution of Individual Chloroplast Genes.- 3.2. General Features of Chloroplast Gene Evolution.- 4. Mitochondrial DNA Evolution.- 4.1. Genome Size.- 4.2. Genome Organization and Intragenomic Recombination.- 4.3. Rearrangement in Evolution.- 4.4. Rearrangement in Cultured Cells and Somatic Crosses.- 4.5. Extrachromosomal Elements in Plant Mitochondria.- 4.6. Gene Content and Gene Transfer.- 4.7. Gene Evolution and Genetic Code.- 5. Phylogenese Implications of Organelle DNA Variation.- 5.1. Endosymbiotic Origins of Chloroplasts and Mitochondria.- 5.2. Phylogenetic Relationships among Plants and Algae.- 6. Summary Comparison of Chloroplast and Mitochondrial DNA Evolution.- References.- 4 Localized Highly Repetitive DNA Sequences in Vertebrate and Invertebrate Genomes.- 1. Introduction.- 1.1. Historical Perspectives: Audi alteram partem.- 2. The Molecular and Biological Data Base: Vertebrates.- 2.1. Kangaroo Rats and the Concept of a Library.- 2.2. Amphibians and the Transcriptional Capacities of Tandem Arrays.- 2.3. The Calf and the Concept of DNA Reamplification.- 2.4. Primate Repeats and DNA Sequence Variation.- 2.5. The Mouse, DNA Polymorphisms, and Chromosome Pairing.- 2.6. Rats and Rearrangements.- 2.7. Sheep, Goats, Satellite Homologies, and Rearrangements.- 3. The Molecular and Biological Data Base: Invertebrates.- 3.1. Drosophila Species.- 3.2. Manipulation of Heterochromatic Regions.- 3.3. Satellite DNA and Development Timing.- 3.4. Evolutionary Considerations.- 3.5. Germ Line Effects.- 3.6. Crabs: From the Simple to the Complex.- 4. Data Summary.- 4.1. Kangaroo Rats.- 4.2. Amphibia.- 4.3. The Calf.- 4.4. Primates.- 4.5. The Mouse.- 4.6. Rats.- 4.7. Sheep and Goats.- 4.8. Drosophila.- 4.9. Grasshoppers.- 4.10. Crabs.- 5. Epilogue.- 5.1. Cellular, Structural, and Mechanistic Approaches.- 5.2. Evolutionary Concepts and Tandem Arrays: Anguillam cauda tenes.- 6. Conclusions.- References.- 5 The Evolution of Interspersed Repetitive DNA Sequences in Mammals and Other Vertebrates.- 1. Introduction.- 2. Background.- 2.1. DNA Renaturation Studies.- 2.2. Summary of Renaturation Studies.- 3. RNA Pseudogenes.- 3.1. Pseudogenes Resulting from Processed mRNA.- 3.2. Small RNA Pseudogenes Are Recognizably Interspersed Repeats.- 4. The Alu Family and Its Allies.- 4.1. Structure of the Human Alu Family.- 4.2. Direct Repeats Flanking Alu Family Members.- 4.3. Nonhuman Alu-like Sequences.- 5. Non-Alu-Family Interspersed Repeats.- 5.1. Kpn/BamH1 Repeats in Primate and Rodent.- 5.2. Other Families of Inserted Repeats.- 5.3. Interspersed Tandem Repeats.- 6. Biological Functions and Effects.- 6.1. Similarity of Inserted Repeats and Pseudogenes.- 6.2. Possible Functions of Alu-like Sequences.- 6.3. Effects Attributable to the Presence and Insertion of Alu.- 6.4. Functions and Effects of Interspersed Tandem Repeats.- 7. Summary.- References.- 6 The Contributions of Retroviruses to the Study of Mammalian Evolution.- 1. Introduction.- 2. Isolation of Primate Retroviruses.- 2.1. Introduction.- 2.2. Comparison of Primate Viral Isolates.- 3. Phylogeny of Primates as Indicated by DNA-DNA Hybridization.- 3.1. Generation Time Effect on the Average Rate of DNA Evolution.- 3.2. Thermal Stability Measurements of Mammalian Species Capable of Producing Viable Hybrids.- 4. Evolution of Primate Retrovirus Genes.- 4.1. Evolution of Baboon Type C Viral Genes.- 4.2. Effect of Geographic Habitat of a Species on the Rate of Baboon Virogene Evolution.- 4.3. Evolution of Languar Type D Viral Genes.- 4.4. Evolution of Colobus, Macaque, Squirrel Monkey, and Owl Monkey Virogenes.- 5. Endogenous Mammalian Retroviruses.- 6. Interspecies Transmission and Germ Line Integration of Mammalian Retroviruses.- 6.1. Transfer of Virus from Baboon Ancestor to Domestic Cat Ancestor.- 6.2. Use of Interspecies Retrovirus Transmission as a Marker for Species Divergence.- 6.3. Interspecies Transmission from Ancestors of Rodents to Cats.- 6.4. Interspecies Transmission from Rodent Ancestors to Ancestors of the Pig.- 6.5. Interspecies Transmission from New World Monkeys to New World Carnivores.- 6.6. Interspecies Transmission from Rodent Ancestors to Ancestors of Minks and Weasels.- 7. Interspecies Transmission of Infectious Retroviruses.- 7.1. Origin of Gibbon Leukemia Virus.- 7.2. Origin of Infectious Macaque Viruses.- 7.3. Mammalian Retroviruses of Unknown Origin.- 7.4. Interspecies Transmission of Nonmammalian Retroviruses.- 8. Conclusion.- References.- 7 Evolution of Ribosomal DNA.- 1. Origin of Genes for the Translational Apparatus.- 1.1. An RNA Basis for the Primitive Translational Machinery.- 1.2. Was There a tRNA Ancestor to rRNA?.- 1.3. Ribosomal Proteins May Be a Later Addition to the Ribosome.- 1.4. Coordinate Regulation of Synthesis of RNA Components of the Ribosome.- 2. Basic Organization of rDNA.- 2.1. Organization of rDNA in Bacteria.- 2.2. Organization of rDNA in Mitochondria.- 2.3. Organization of rDNA in Chloroplasts.- 2.4. Organization of rDNA in Eukaryotic Nuclei.- 3. Evolutionary Conservation in rRNA Structure.- 3.1. Primary Structure of rRNA.- 3.2. Secondary Structure of rRNA.- 4. Processing of rRNA.- 4.1. rRNA Processing in Eubacteria.- 4.2. rRNA Processing in Eukaryotes.- 5. Nontranscribed Spacers.- 5.1. Length Variability and Sequence Repetition in the NTS.- 5.2. Functional Regions within the NTS.- 6. Evolutionary Forces Acting on rDNA.- 6.1. The Riddle of Concerted Evolution.- 6.2. Mechanisms of Molecular Drive.- 6.3. Selection Superimposed on Molecular Drive.- References.- 8 On the Evolution of Genome Organization in Mammals.- 1. Introduction.- 2. Procedures for Studying Genome Evolution.- 3. The Human Gene Map: An Index Species.- 4. Comparative Genetics and Cytogenetics of Primates.- 4.1. The Great Apes.- 4.2. Comparative Mapping of Man and Other Primates.- 4.3. Primate Gene Families.- 5. Comparative Genetics and Cytogenetics of Rodents.- 5.1. Comparative Genetics within Rodentia.- 5.2. Comparative Genetics between Rodents and Primates.- 6. Comparative Genetics and Cytogenetics of Carnivores.- 6.1. The Cat Family, Felidae.- 6.2. Other Carnivores.- 7. Other Mammalian Families.- 8. Endogenous Retroviruses.- 9. Comparative Genetics of Mammalian Oncogenes.- 10. Conclusions.- References.