Note: Front Cover -- Molecular Systematics of Fishes -- Copyright Page -- Contents -- Contributors -- Preface -- Chapter 1. Molecules and Morphology in Studies of Fish Evolution -- I. Introduction -- II. History of Molecular Techniques -- III. Controversy over Analytical Methods -- IV. Achievements and Failures of Molecular Systematics -- V. Eight Promising Directions for Future Research -- VI. A New Age of Synthesis -- References -- Chapter 2. Base Substitution in Fish Mitochondrial DNA: Patterns and Rates -- I. Introduction -- II. Simple Models of Substitution -- III. Evolution of Real Sequences -- IV. Implications for Phylogenetic Reconstruction -- V. Conclusions -- References -- Chapter 3. Molecular Systematics of a Rapidly Evolving Species Flock: The mbuna of Lake Malawi and the Search for Phylogenetic Signal -- I. Introduction -- II. Molecular Investigations -- III. Mitochondrial DNA and Ancestral Polymorphisms -- IV. Alternate Molecular Approaches -- V. Microsatellite Loci -- VI. A Test of the Phylogenetic Potential of Microsatellites -- VII. Materials and Methods -- VIII. Results -- IX. Discussion -- X. Summary -- References -- Chapter 4. Reconstruction of Cichlid Phylogeny Using Nuclear DNA Markers -- I. Introduction -- II. Methods Used for Reconstructing Cichlid Phylogeny -- III. Random Amplification of Polymorphic DNA (RAPD) -- IV. Allele Size Frequencies at Dinucleotide Microsatellite Loci -- V. Critical Evaluation Using RAPD and Microsatellite Allele Frequencies for the Reconstruction of Cichlid Fish Phylogeny -- References -- Chapter 5. Biogeographic Analysis of Pacific Trout (Oncorhynchus mykiss) in California and Mexico Based on Mitochondrial DNA and Nuclear Microsatellites -- I. Introduction -- II. Materials and Methods -- III. Results -- IV. Discussion -- References -- Appendices. , Chapter 6. Mitochondrial DNA Sequence Variation among the Sand Darters (Percidae: Teleostei) -- I. Introduction -- II. Systematics of Sand Darters -- III. Methods and Materials -- IV. Results -- V. Discussion -- VI. Summary -- References -- Appendices -- Chapter 7. Phylogeographic Patterns in Populations of Cichlid Fishes from Rocky Habitats in Lake Tanganyika -- I. Lake Tanganyika and Its Cichlid Species Flock -- II. Speciation and DNA -- III. From Patterns toward an Understanding of Processes -- IV. Conclusions -- References -- Chapter 8. Fish Biogeography and Molecular Clocks: Perspectives from the Panamanian Isthmus -- I. Introduction -- II. Temporal Scaling: The Panama Isthmus and Molecular Clocks -- III. Geographic Scaling: The Panama Isthmus and Caribbean Fish -- IV. Geographic Scaling: The Panama Isthmus and the Circumtropical Abudefduf (Teleostei: Pomacentridae) Species Group -- V. Geographic Scaling: The Panama Isthmus and Neotropical Freshwater Fishes -- VI. Concluding Remarks -- References -- Chapter 9. The Utility of Mitochondrial DNA Control Region Sequences for Analyzing Phylogenetic Relationships among Populations, Species, and Genera of the Percidae -- I. Introduction -- II. Materials and Methods -- III. Results -- IV. Discussion -- V. Material Examined -- References -- Chapter 10. Phylogenetic Relationships among the Salmoninae Based on Nuclear and Mitochondrial DNA Sequences -- I. Introduction -- II. Conclusions -- References -- Chapter 11. Combining Molecular and Morphological Data in Fish Systematics: Examples from the Cyprinodontiformes -- I. Introduction -- II. Analysis of Combined Data: Justification -- III. Analysis of Combined Data: Methods -- IV. Consensus Approaches: Justification -- V. Consensus Methods -- VI. Analysis of Cyprinodontiform Data -- VII. Methods -- VIII. Results and Discussion -- IX. Conclusions. , References -- Appendices -- Chapter 12. Molecular Phylogeny of the Fundulidae (Teleostei, Cyprinodontiformes) Based on the Cytochrome b Gene -- I. Introduction -- II. Morphology -- III. Allozymes and DNA -- IV. Fish Samples -- V. DNA Sequences -- VI. Phylogenetic Relationships -- VII. Conclusion -- References -- Chapter 13. Interrelationships of Lamniform Sharks: Testing Phylogenetic Hypotheses with Sequence Data -- I. Introduction -- II. Materials and Methods -- III. Results and Discussion -- References -- Appendix -- Chapter 14. Radiation of Characiform Fishes: Evidence from Mitochondrial and Nuclear DNA Sequences -- I. Introduction -- II. Materials and Methods -- III. Results and Discussion -- References -- Appendix -- Chapter 15. The Evolution of Blennioid Fishes Based on an Analysis of Mitochondrial 12S rDNA -- I. Introduction -- II. Materials and Methods -- III. Results -- IV. Discussion -- V. Summary -- References -- Chapter 16. Major Histocompatibility Complex Genes in the Study of Fish Phylogeny -- I. Introduction -- II. Major Histocompatibility Complex (Mhc) Structure and Function -- III. Mhc as a Source of Systematic Information -- IV. Sequences as a Source of Phylogenetic and Systematic Information -- V. Cladistic Analysis with Macromutations -- VI. Mhc Gene Frequencies in Populations Undergoing Adaptive Radiation -- VII. Conclusion -- References -- Chapter 17. The Phylogenetic Utility of the Mitochondrial Cytochrome b Gene for Inferring Relationships among Actinopterygian Fishes -- I. Introduction -- II. Materials and Methods -- III. Results and Discussion -- References -- Taxonomic Index -- Subject Index -- Color Plate Section.