Macromolecular Sequences in Systematic and Evolutionary Biology

ISBN-13: 9781468442854 / Angielski / Miękka / 2012 / 418 str.

Morris Goodman

Opis

George H. F. Nuttall pioneered the study of phylogeny through the ge- netically encoded sequence structures of proteins. His classic monograph, Blood Immllnity and Blood Relationship, was published in 1904. The findings described in this monograph testified that immunologic compar- isons of serum proteins could help reveal the phyletic relationships of primates and other animals. Although Nuttall had no way of knowing that a correspondence between the nucleotide sequences of genes and the amino acid sequences of proteins was the genetic basis for the immuno- logic specificities of animal sera, he clearly saw the implications of his findings. Thus he wrote in the introduction of his monograph, "The per- sistence of the chemical blood-relationship between the various groups of animals serves to carry us back into geological times, and I believe we have but begun the work along these lines, and that it will lead to valuable results in the study of various problems of evolution. " Nuttall's prophecy is being fulfilled. Through the first two-thirds of the 20th century immu- nology led the way in the molecular analysis of the phyletic relationships of animal taxa above the species level. Amino acid sequencing of proteins began in earnest during the 1960s. It overtook immunology during the 1970s and provided more exact molecular data for investigating the history of life and the forces of chance and selection which drive evolution.

Spis treści

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.