Contributors

Preface

CHAPTER 1 Molecules and Morphology in Studies of Fish Evolution

Carol A. Stepien

Thomas D. Kocher

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

Thomas D. Kocher

Karen L. Carleton

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

Irv Kornfield

Alex Parker

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

Holger Siiltmann

Werner E. Mayer

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

Jennifer L. Nielsen

Monique C. Fountain

Jonathan M. Wright

I. Introduction

II. Materials and Methods

III. Results

IV. Discussion

References

Appendices

CHAPTER 6 Mitochondrial DNA Sequence Variation among the Sand Darters (Percidae: Teleostei)

E. O. Wiley

Robert H. Hagen

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 Rockey Habitats in Lake Tanganyika

Christian Sturmbauer

Erik Verheyen

Lukas Riiber

Axel Meyer

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

Eldredge Bermingham

S. Shawn McCafferty

Andrew P. Martin

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

Joseph E. Faber

Carol A. Stepien

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

Ruth B. Phillips

Todd H. Oakley

I. Introduction

II. Conclusions

References

CHAPTER 11 Combining Molecular and Morphological Data in Fish Systematics: Examples from the Cyprinodontiformes

Alex Parker

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

Giacomo Bernardi

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

Gavin J. P. Naylor

Andrew P. Martin

Erik G. Mattison

Wesley M. Brown

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

Guillermo Orti

I. Introduction

II. Meterials and Methods

III. Results and Discussion

References

Appendix

CHAPTER 15 The Evolution of Blennioid Fishes Based on an Analysis of Mitochondrial 12S rDNA

Carol A. Stepien

Alison K. Dillon

Meriel J. Brooks

Kristen L. Chase

Allyson N. Hubers

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

Jan Klein

Dagmar Klein

Felipe Figueroa

Akie Sato

Colm O'hUigin

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

Charles Lydeard

Kevin J. Roe

I. Introduction

II. Materials and Methods

III. Results and Discussion

References

Taxonomic Index

Subject Index