Molecular Systematics of Fishes

, by Kocher, Thomas D.; Stepien, Carol A.

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ISBN: 9780124175402 | 0124175406
Cover: Hardcover
Copyright: 5/1/1997

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Sequenced biological macromolecules have revitalized systematic studies of evolutionary history. Molecular Systematics of Fishes is the first authoritative overview of the theory and application of these sequencing data to fishes. This volume explores the phylogeny of fishes at multiple taxonomic levels, uses methods of analysis of molecular data that apply both within and between fish populations, and employs molecule-based phylogenies to address broader questions of evolution. Targeted readers include ichthyologists, marine scientists, and all students, faculty, and researchers interested in fish evolution and ecology and vertebrate systematics.

Contributors

(2)

Preface

CHAPTER 1 Molecules and Morphology in Studies of Fish Evolution

(12)

Carol A. Stepien

Thomas D. Kocher

I. Introduction

(1)

II. History of Molecular Techniques

(3)

III. Controversy over Analytical Methods

(2)

IV. Achievements and Failures of Molecular Systematics

(1)

V. Eight Promising Directions for Future Research

(1)

VI. A New Age of Synthesis

(1)

References

(4)

CHAPTER 2 Base Substitution in Fish Mitochondrial DNA: Patterns and Rates

(12)

Thomas D. Kocher

Karen L. Carleton

I. Introduction

(1)

II. Simple Models of Substitution

(2)

III. Evolution of Real Sequences

(4)

IV. Implications for Phylogenetic Reconstruction

(4)

V. Conclusions

(1)

References

(1)

CHAPTER 3 Molecular Systematics of a Rapidly Evolving Species Flock: The mbuna of Lake Malawi and the Search for Phylogenetic Signal

(14)

Irv Kornfield

Alex Parker

I. Introduction

(1)

II. Molecular Investigations

(1)

III. Mitochondrial DNA and Ancestral Polymorphisms

(1)

IV. Alternate Molecular Approaches

(1)

V. Microsatellite Loci

(1)

VI. A Test of the Phylogenetic Potential of Microsatellites

(2)

VII. Materials and Methods

(1)

VIII. Results

(1)

IX. Discussion

(2)

X. Summary

(1)

References

(4)

CHAPTER 4 Reconstruction of Cichlid Phylogeny Using Nuclear DNA Markers

(14)

Holger Siiltmann

Werner E. Mayer

I. Introduction

(1)

II. Methods Used for Reconstructing Cichlid Phylogeny

(1)

III. Random Amplification of Polymorphic DNA (RAPD)

(4)

IV. Allele Size Frequencies at Dinucleotide Microsatellite Loci

(2)

V. Critical Evaluation Using RAPD and Microsatellite Allele Frequencies for the Reconstruction of Cichlid Fish Phylogeny

(2)

References

(4)

CHAPTER 5 Biogeographic Analysis of Pacific Trout (Oncorhynchus mykiss) in California and Mexico Based on Mitochondrial DNA and Nuclear Microsatellites

(22)

Jennifer L. Nielsen

Monique C. Fountain

Jonathan M. Wright

I. Introduction

(2)

II. Materials and Methods

(2)

III. Results

(7)

IV. Discussion

(2)

References

(4)

Appendices

(5)

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

(22)

E. O. Wiley

Robert H. Hagen

I. Introduction

(1)

II. Systematics of Sand Darters

(2)

III. Methods and Materials

(1)

IV. Results

(13)

V. Discussion

(3)

VI. Summary

(1)

References

(2)

Appendices

(1)

CHAPTER 7 Phylogeographic Patterns in Populations of Cichlid Fishes from Rockey Habitats in Lake Tanganyika

(16)

Christian Sturmbauer

Erik Verheyen

Lukas Riiber

Axel Meyer

I. Lake Tanganyika and Its Cichlid Species Flock

(1)

II. Speciation and DNA

(7)

III. From Patterns toward an Understanding of Processes

105

(4)

IV. Conclusions

109

(1)

References

109

(4)

CHAPTER 8 Fish Biogeography and Molecular Clocks: Perspectives from the Panamanian Isthmus

113

(16)

Eldredge Bermingham

S. Shawn McCafferty

Andrew P. Martin

I. Introduction

113

(1)

II. Temporal Scaling: The Panama Isthmus and Molecular Clocks

114

(5)

III. Geographic Scaling: The Panama Isthmus and Caribbean Fish

119

(2)

IV. Geographic Scaling: The Panama Isthmus and the Circumtropical Abudefduf (Teleostei: Pomacentridae) Species Group

121

(2)

V. Geographic Scaling: The Panama Isthmus and Neotropical Freshwater Fishes

123

(2)

VI. Concluding Remarks

125

(1)

References

126

(3)

CHAPTER 9 The Utility of Mitochondrial DNA Control Region Sequences for Analyzing Phylogenetic Relationships among Populations, Species, and Genera of the Percidae

129

(16)

Joseph E. Faber

Carol A. Stepien

I. Introduction

129

(2)

II. Materials and Methods

131

(2)

III. Results

133

(4)

IV. Discussion

137

(3)

V. Material Examined

140

(1)

References

140

(5)

CHAPTER 10 Phylogenetic Relationships among the Salmoninae Based on Nuclear and Mitochondrial DNA Sequences

145

(18)

Ruth B. Phillips

Todd H. Oakley

I. Introduction

145

(13)

II. Conclusions

158

(1)

References

159

(4)

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

163

(26)

Alex Parker

I. Introduction

163

(1)

II. Analysis of Combined Data: Justification

164

(1)

III. Analysis of Combined Data: Methods

165

(1)

IV. Consensus Approaches: Justification

166

(1)

V. Consensus Methods

166

(1)

VI. Analysis of Cyprinodontiform Data

167

(1)

VII. Methods

167

(3)

VIII. Results and Discussion

170

(11)

IX. Conclusions

181

(1)

References

182

(2)

Appendices

184

(5)

CHAPTER 12 Molecular Phylogeny of the Fundulidae (Teleostei, Cyprinodontiformes) Based on the Cytochrome b Gene

189

(10)

Giacomo Bernardi

I. Introduction

189

(1)

II. Morphology

190

(1)

III. Allozymes and DNA

191

(1)

IV. Fish Samples

191

(1)

V. DNA Sequences

191

(2)

VI. Phylogenetic Relationships

193

(2)

VII. Conclusion

195

(1)

References

195

(4)

CHAPTER 13 Interrelationships of Lamniform Sharks: Testing Phylogenetic Hypotheses with Sequence Data

199

(20)

Gavin J. P. Naylor

Andrew P. Martin

Erik G. Mattison

Wesley M. Brown

I. Introduction

199

(3)

II. Materials and Methods

202

(2)

III. Results and Discussion

204

(12)

References

216

(2)

Appendix

218

(1)

CHAPTER 14 Radiation of Characiform Fishes: Evidence from Mitochondrial and Nuclear DNA Sequences

219

(26)

Guillermo Orti

I. Introduction

219

(3)

II. Meterials and Methods

222

(1)

III. Results and Discussion

222

(18)

References

240

(2)

Appendix

242

(3)

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

245

(26)

Carol A. Stepien

Alison K. Dillon

Meriel J. Brooks

Kristen L. Chase

Allyson N. Hubers

I. Introduction

245

(5)

II. Materials and Methods

250

(3)

III. Results

253

(5)

IV. Discussion

258

(9)

V. Summary

267

(1)

References

268

(3)

CHAPTER 16 Major Histocompatibility Complex Genes in the Study of Fish Phylogeny

271

(14)

Jan Klein

Dagmar Klein

Felipe Figueroa

Akie Sato

Colm O'hUigin

I. Introduction

271

(1)

II. Major Histocompatibility Complex (Mhc) Structure and Function

271

(2)

III. Mhc as a Source of Systematic Information

273

(1)

IV. Sequences as a Source of Phylogenetic and Systematic Information

273

(2)

V. Cladistic Analysis with Macromutations

275

(1)

VI. Mhc Gene Frequencies in Populations Undergoing Adaptive Radiation

276

(3)

VII. Conclusion

279

(2)

References

281

(4)

CHAPTER 17 The Phylogenetic Utility of the Mitochondrial Cytochrome b Gene for Inferring Relationships among Actinopterygian Fishes

285

(20)

Charles Lydeard

Kevin J. Roe

I. Introduction

285

(3)

II. Materials and Methods

288

(1)

III. Results and Discussion

289

(11)

References

300

(5)

Taxonomic Index

305

(6)

Subject Index

311

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Molecular Systematics of Fishes

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