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| Background | |
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| Introduction | |
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| Why Employ Molecular Genetic Markers? | |
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| Molecular data are genetic | |
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| Molecular methods open the entire biological world for genetic scrutiny | |
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| Molecular methods access a nearly unlimited pool of genetic variability | |
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| Molecular data can distinguish homology from analogy | |
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| Molecular data provide common yardsticks for measuring divergence | |
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| Molecular approaches facilitate mechanistic appraisals of evolution | |
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| Molecular approaches are challenging and exciting | |
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| Why Not Employ Molecular Genetic Markers? | |
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| The History of Interest in Genetic Variation | |
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| The Classical--Balance Debate | |
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| Classical versus balance views of genome structure | |
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| Molecular input to the debate | |
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| Questions of empirical refinement | |
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| The Neutralist--Selectionist Debate | |
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| Multi-locus allozyme heterozygosity and organismal fitness | |
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| Single-locus allozyme variation and the vertical approach | |
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| Selection at the level of DNA | |
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| The unresolved status of the controversy | |
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| Must Molecular Markers Be Neutral To Be Informative? | |
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| The Molecule--Morphology Debate | |
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| Molecular Phylogenetics | |
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| Molecular Techniques | |
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| Protein Immunology | |
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| Protein Electrophoresis | |
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| Mendelian markers | |
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| Idiosyncratic protein features | |
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| DNA--DNA Hybridization | |
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| Restriction Analyses | |
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| Animal mitochondrial DNA | |
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| Plant organelle DNA | |
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| Single-copy nuclear DNA | |
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| Moderately repetitive gene families | |
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| Minisatellites and DNA fingerprinting | |
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| Polymerase Chain Reaction | |
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| RAPDs | |
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| STRs (microsatellites) | |
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| AFLPs | |
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| SINEs | |
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| SSCPs | |
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| SNPs | |
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| HAPSTRs and SNPSTRs | |
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| DNA sequencing | |
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| Categorical Breakdowns of Molecular Methods | |
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| Protein versus DNA information | |
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| Discrete versus distance data | |
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| Detached versus connectable information | |
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| Single-locus versus multi-locus data | |
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| Utility of data along the phylogenetic hierarchy | |
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| Philosophies and Methods of Molecular Data Analysis | |
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| Cladistics versus Phenetics | |
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| Molecular Clocks | |
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| History of clock calibrations and controversies | |
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| Absolute and relative rate comparisons | |
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| Closing thoughts on clocks | |
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| Phylogenetic Reconstruction | |
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| Distance-based approaches | |
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| Character-state approaches | |
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| Conclusions about phylogenetic procedures | |
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| Gene Trees versus Species Trees | |
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| Applications | |
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| Individuality and Parentage | |
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| Human Forensics | |
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| History of laboratory approaches | |
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| History of controversies | |
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| Empirical examples | |
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| Ramets and Genets | |
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| Background | |
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| Spatial Distributions of Clones | |
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| Ages of clones | |
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| Clonal reproduction in microorganisms | |
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| Genetic chimeras | |
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| Gender Ascertainment | |
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| Genetic Parentage | |
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| Behavioral and evolutionary contexts | |
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| Selected empirical examples by taxa | |
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| Selected empirical examples by topic | |
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| Kinship and Intraspecific Genealogy | |
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| Close Kinship and Family Structure | |
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| Eusocial colonies | |
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| Non-eusocial groups | |
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| Kin recognition | |
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| Genetic relationships of specific individulas | |
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| Geographic Population Structure and Gene Flow | |
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| Autogamous mating systems | |
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| Gametic and zygotic dispersal | |
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| Direct estimates of dispersal distances | |
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| Vagility, philopatry, and dispersal scale | |
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| Non-neutrality of some molecular markers | |
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| Historical demographic events | |
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| Population assignments | |
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| Phylogeography | |
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| History and background | |
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| Case studies on particular populations or species | |
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| Genealogical concordance | |
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| Genealogical discordance | |
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| Microtemporal Phylogeny | |
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| Speciation and Hybridization | |
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| The Speciation Process | |
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| How much genetic change accompanies speciation? | |
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| Do founder-induced speciations leave definitive genetic signatures? | |
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| What other kinds of phylogenetic signatures do past speciations provide? | |
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| Are speciation rates and divergence rates correlated? | |
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| Can speciation occur sympatrically? | |
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| What are the temporal durations of speciation processes? | |
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| How prevalent is co-speciation? | |
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| Can morphologically cryptic species be diagnosed? | |
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| Should a phylogenetic species concept replace the BSC? | |
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| Hybridization and Introgression | |
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| Frequencies and geographic settings of hybridization | |
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| Sexual asymmetries in hybrid zones | |
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| More hybrid zone asymmetries | |
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| More hybrid zone phenomena | |
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| Speciation by hybridization | |
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| Species Phylogenies and Macroevolution | |
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| Rationales for Phylogeny Estimation | |
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| Phylogenetic character mapping | |
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| Biogeographic assessment | |
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| Academic pursuit of genealogical roots | |
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| Some Special Topics in Phylogeny Estimation | |
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| DNA hybridization and avian systematics | |
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| Mitochondrial DNA and the higher systematics of animals | |
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| Chloroplast DNA and the higher systematics of plants | |
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| Ribosomal gene sequences and deep phylogenies | |
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| Genomic Mergers, DNA Transfers, and Life's Early History | |
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| From ancient endosymbioses to recent intergenomic transfers | |
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| Horizontal gene transfer | |
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| Relationships between retroviruses and transposable elements | |
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| Further Topics in Molecular Phylogenetics | |
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| Toward a global phylogeny and universal systematics | |
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| Molecular paleontology | |
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| Molecular Markers in Conservation Genetics | |
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| Within-Population Heterozygosity Issues | |
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| Molecular variability in rare and threatened species | |
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| Does reduced molecular variability matter? | |
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| Genealogy at the Microevolutionary Scale | |
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| Tracking individuals in wildlife management | |
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| Parentage and kinship | |
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| Gender identification | |
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| Estimating historical population size | |
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| Dispersal and gene flow | |
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| Population Structure and Phylogeography | |
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| Genetics-demography connections | |
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| Inherited versus acquired markers | |
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| Mixed-stock assessment | |
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| Shallow versus deep population structures | |
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| Lessons from intraspecific phylogeography | |
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| Issues At and Beyond the Species Level | |
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| Speciation and conservation biology | |
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| Hybridization and introgression | |
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| Species phylogenies and macroevolution | |
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| Conclusion | |
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| Literature Cited | |
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| Taxonomic Index | |
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| Subject Index | |