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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 | |