Molecular Markers, Natural History, and Evolution

ISBN-10: 0878930418
ISBN-13: 9780878930418
Edition: 2nd 2004
Authors: John C. Avise
List price: $59.95
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Book details

List price: $59.95
Edition: 2nd
Copyright year: 2004
Publisher: Sinauer Associates, Incorporated
Binding: Paperback
Pages: 684
Size: 7.00" wide x 9.00" long x 1.00" tall
Weight: 2.486
Language: English

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

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