Molecular Markers, Natural History and Evolution: Natural History and EvolutionMolecular approaches have opened new windows on a host of ecological and evolutionary disciplines, ranging from population genetics and behavioral ecology to conservation biology and systematics. Molecular Markers, Natural History and Evolution summarizes the multi-faceted discoveries about organisms in nature that have stemmed from analyses of genetic markers provided by polymorphic proteins and DNAs. The first part of the book introduces rationales for the use of molecular markers, provides a history of molecular phylogenetics, and describes a wide variety of laboratory methods and interpretative tools in the field. The second and major portion of the book provides a cornucopia of biological applications for molecular markers, organized along a scale from micro-evolutionary topics (such as forensics, parentage, kinship, population structure, and intra-specific phylogeny) to macro-evolutionary themes (including species relationships and the deeper phylogenetic structure in the tree of life). Unlike most prior books in molecular evolution, the focus is on organismal natural history and evolution, with the macromolecules being the means rather than the ends of scientific inquiry. Written as an intellectual stimulus for the advanced undergraduate, graduate student, or the practicing biologist desiring a wellspring of research ideas at the interface of molecular and organismal biology, this book presents material in a manner that is both technically straightforward, yet rich with concepts and with empirical examples from the world of nature. |
Contents
Introduction | 3 |
WHY EMPLOY MOLECULAR GENETIC MARKERS? | 5 |
Molecular Methods Open the Entire Biological World for Genetic Scrutiny | 6 |
Molecular Data Can Distinguish Homology from Analogy | 8 |
Molecular Data Provide Common Yardsticks for Measuring Divergence | 9 |
Molecular Approaches Facilitate Mechanistic Appraisals of Evolution | 11 |
Molecular Approaches are Challenging and Exciting | 12 |
WHY NOT EMPLOY MOLECULAR GENETIC MARKERS? | 15 |
Marine Gametes and Larvae | 215 |
Direct Estimates of Dispersal Distances | 221 |
Vagility Philopatry and Dispersal Scale | 222 |
Physical Dispersal Barriers | 223 |
Philopatry to Natal Site | 224 |
Genderbiased Dispersal and Gene Flow | 227 |
Nonneutrality of Some Molecular Markers | 230 |
Historical Demographic Events | 232 |
History of Molecular Phylogenetics | 16 |
DEBATES AND DIVERSIONS FROM MOLECULAR SYSTEMATICS | 17 |
Molecular Input to the Debate | 20 |
Research Preoccupations of the ProteinElectrophoretic Revolution | 22 |
Empirical Approaches to the VariabilityFitness Conundrum | 23 |
Genetic Theory and the NeutralistSelectionist Debate | 26 |
Systematic Philosophy and the PheneticCladistic Debate | 34 |
Phylogenetic Data and the MoleculeMorphology Debate | 39 |
MOLECULAR PHYLOGENETICS | 40 |
SUMMARY | 43 |
Molecular Tools | 44 |
Data | 46 |
Protein Electrophoresis | 47 |
Data | 49 |
DNA ASSAYS | 53 |
Data | 55 |
Restriction Analyses | 57 |
Animal Mitochondrial DNA | 60 |
Plant Mitochondrial and Chloroplast DNA | 68 |
Singlecopy Nuclear DNA | 69 |
Ribosomal RNA Genes and other Middlerepetitive Gene Families | 75 |
Minisatellite Sequences and DNA Fingerprinting | 78 |
DNA Sequencing and the Polymerase Chain Reaction | 82 |
Data | 87 |
REFERENCES TO LABORATORY PROTOCOLS | 90 |
SUMMARY | 91 |
Interpretive Tools | 92 |
Protein Versus DNA Information | 93 |
Detached versus Connective Information | 97 |
Utility of Data Along the Phylogenetic Hierarchy | 98 |
MOLECULAR CLOCKS | 100 |
Clock Calibrations and Controversies | 103 |
Absolute and Relative Rate Comparisons | 106 |
Closing Thoughts About Molecular Clocks | 108 |
PROCEDURES FOR PHYLOGENY RECONSTRUCTION | 109 |
Distance Approaches | 111 |
FitchMargoliash Method | 113 |
NeighborJoining Method | 114 |
Distance Wagner Method | 115 |
Comparison of Distance Matrix Methods | 119 |
CharacterState Approaches | 120 |
Hennigian Cladistics | 121 |
Maximum Parsimony | 122 |
Conclusions About Phylogenetic Procedures | 124 |
GENE TREES VERSUS SPECIES TREES | 126 |
SUMMARY | 138 |
Applications | 139 |
Individuality and Parentage | 141 |
Ramets and Genets | 147 |
Spatial Distributions of Clones | 150 |
Ages of Clones | 155 |
Genetic Mosaics | 159 |
Clonal Reproduction in Microorganisms | 160 |
Gender Determination | 167 |
PARENTAGE | 168 |
Paternity Analysis | 172 |
Paternity in Plants | 177 |
Sperm and Pollen Competition Precedence | 182 |
Maternity Analysis | 185 |
SUMMARY | 188 |
Kinship and Intraspecific Phylogeny | 190 |
Eusocial Colonies | 194 |
Noneusocial Colonies and Groups | 199 |
Kin Recognition | 203 |
GEOGRAPHIC POPULATION STRUCTURE AND GENE FLOW | 204 |
Autogamous Mating Systems | 210 |
Gametic and Zygotic Dispersal | 213 |
PHYLOGEOGRAPHY | 233 |
Case Histories | 236 |
Interbrood Switching in Periodical Cicadas | 237 |
Natural Selection and Biogeographic History in the Killifish | 238 |
Genealogical Concordance and the Sharptailed Sparrow | 241 |
Phylogeography of a Regional Fauna | 242 |
General Conclusions About Intraspecific Phytogeography | 246 |
MICROTEMPORAL PHYLOGENY | 248 |
SUMMARY | 250 |
Speciation and Hybridization | 252 |
THE SPECIATION PROCESS | 257 |
Molecular Evidence | 261 |
Do Speciations Entail Severe Population Bottlenecks? | 264 |
Are Speciation Rates and Divergence Rates Correlated? | 267 |
Can Speciation Occur Sympatrically? | 269 |
Host or HabitatSwitching in Insects | 272 |
Can Related Species Be Diagnosed Reliably? | 274 |
Should a Phylogenetic Species Concept Replace the BSC? | 278 |
HYBRIDIZATION AND INTROGRESSION | 280 |
Case History Involving Treefrogs | 284 |
Hybrid Zone Asymmetries | 287 |
Haldanes Rule | 289 |
Differential Mating Behaviors | 291 |
Differential Gametic Exchange | 293 |
Reticulate Evolution Evidenced by cpDNA Phylogenies | 295 |
Speciation by Hybridization | 297 |
Origins of Unisexual Biotypes | 299 |
SUMMARY | 305 |
Species Phylogenies and Macroevolution | 306 |
RATIONALES FOR PHYLOGENY ESTIMATION | 307 |
Anatomical Features | 308 |
Behavioral Physiological and Life History Features | 315 |
Biogeographic Assessment | 321 |
Common Ancestry Versus Convergence | 326 |
Recent Islands Ancient Inhabitants | 328 |
Academic Pursuit of Genealogical Roots | 329 |
SPECIAL APPROACHES TO PHYLOGENY ESTIMATION | 331 |
Mitochondrial DNA and the Higher Systematics of Animals | 334 |
mtDNA Sequences | 336 |
Chloroplast DNA and the Higher Systematics of Plants | 337 |
cpDNA Restriction Sites and Sequences | 339 |
Slowly Evolving Gene Sequences and Deep Phytogenetic Branches | 341 |
PROSPECTUS FOR A GLOBAL PHYLOGENY | 350 |
SPECIAL TOPICS IN MOLECULAR PHYLOGENETICS | 352 |
Phylogeny of Retroviruses and Transposable Elements | 354 |
Molecular Paleontology | 356 |
SUMMARY | 359 |
Conservation Genetics | 361 |
ISSUES OF HETEROZYGOSITY | 362 |
Does Reduced Molecular Heterozygosity Matter? | 366 |
ISSUES OF PHYLOGENY | 370 |
Parentage and Kinship | 371 |
Population Structure and Intraspecific Phytogeny | 372 |
Genetic Partitions Within Rare and Threatened Species | 373 |
Stock Identification | 375 |
Conclusions About Intraspecific Phylogeography | 380 |
Speciation and Conservation Biology | 382 |
Molecular Forensics and Law Enforcement | 386 |
Hybridization and Introgression | 388 |
Legal Issues | 391 |
Species Phytogenies and Macroevolution | 393 |
SUMMARY | 396 |
CONCLUSION | 397 |
Literature Cited | 399 |
501 | |
507 | |
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Common terms and phrases
A.C. Wilson Acad allele frequencies allozyme Amer analysis animal approaches assays Ayala behavior Biochemical Biol biology birds characters chloroplast chromosome clade cladistic clonal clones cpDNA differences diploid dispersal DNA fingerprinting DNA sequences DNA-DNA hybridization Drosophila Ecol electrophoretic enzyme estimated eukaryotes eusocial evidence Evol evolutionary example females fishes gene flow gene tree genetic differentiation genetic distances genetic markers genetic structure genetic variation genome genotypes geographic groups haplotypes Heredity heterozygosity human inbreeding individuals intraspecific introgression involves isolated J.C. Avise larvae lineages loci locus males marine mating system methods mitochondrial DNA molecular clock molecular data molecular evolution molecular genetic molecular markers morphological mtDNA multilocus multiple mutation Natl natural populations nuclear genes nucleotide organismal origin OTUs patterns phylogenetic phylogeny plant polymorphisms population genetic population structure Proc protein recombination relatedness relationships reproductive restriction revealed RFLP ribosomal Selander speciation species sperm studies Syst taxa taxonomic unisexual Univ variability versus vertebrates