John C. Avise
（2000年刊行，Harvard University Press，ISBN:0674666380）
【目次】原書よりは詳細です。
Preface
Part 1: History and conceptual background
This section introduces the meaning and purview of phylogeography, describes the history of the discipline on both the empirical and theoretical sides, and highlights novel perspectives that the field has spawned. It concentrates in particular on the tight connections between genealogy and population demography, and the nonequilibrium (i.e., historical) nature ofpopulation genetics.
Chapter 1. The history and purview of phylogeography
Empirical roots of mitochondrial DNA research
Preludes to phylogeographic efforts
Pioneering phylogeographic studies
Subsequent mitchondrial findings
Intercellular populations of molecules
Heteroplasmy
Paternal leakage
Mitochondrial DNA clocks
Influential reviews on mtDNA evolution
Conceptual roots of coalescent theory
Other recent developments
Summary
Chapter 2. Demography-phylogeny connections
Intra-population matrilines
Branching processes and coalescent theory
Related perspectives from inbreeding theory:
generational times to coancestry
Evolutionary effective population size
Dynamics of population size
Extensions to spatially structured populations
Isolated populations
Retentions of ancient lineages
Phylogenetic categories of relationship
Short-period isolations
Intermediate situations
Tradistional approaches to gene-flow estimation
Phylogeographic statistics
Extentions to nuclear genealogies
The concept of nuclear gene trees
Empirical complications
Technical hurdles
Biological hurdles
Matrilines: a special connection
between phylogeny and demography
Summary
Part 2: Empirical intraspecific phylogeography
Theories of lineage sorting and the coalescent indicate that a great diversity of intraspecific phylogeographic patterns might be anticipated as functions of species' varied demographic histories. Empirical findings (primarily from mt DNA assays) appear to have borne this out. This section illustrates the wide assortment of idiosyncratic phylogeographic patterns documented to date. It asks whether general trends nontheless have emerged that carry predictive power in relating comparative phylogeographic patterns across taxa to particular categories of natural history or environmental circumstance.
Chapter 3. Lessons from human analysis
Refinements of demographic interpretations
Historical population size
MtDNA assessments
Nuclear genealogical assessments
The questions of African origins
Other genealogical studies
Regional populations
Peopling of the animals
Histories of other areas
Local migratory and mating patterns
The Neanderthals
Summary
Chapter 4. Intraspecific patterns in other animals
Phylogeographic hypotheses
Category 1: Deep gene tree, major lineages allopatric
Category 2: Deep gene tree, major lineages broadly sympatric
Category 3: Shallow gene tree, lineages allopatric
Category 4: Shallow gene tree, lineages sympatric
Category 5: Shallow gene tree, lineage distributions varied
Mammals
Small-bodied terrestrial species
Large bodied terrestrial species
Volant species
Marine species
Birds
Reptiles and amphibians
Terrestrial and freshwater species
Unisexuals
Marine turtles
Fishes
Freshwater fishes
Marine fishes
Diadromous species
Invertebrates
Terrestrial and aerial species
Freshwater species
Marine species
Summary
Part 3: Genealogical concordance: Toward speciation and beyond
Much of the effort of empirical phylogeography summarized in Part 2 involved molecular examinations of the genealogical histories of single genes (usually mtDNA) in particular species, one at a time. The third section of this book extends such approaches to multiple genes, multiple codistributed species, and comparisons with more traditional kinds of biogeographic data. Such extensions into comparative phylogeography introduce several distinct aspects of genealogical concordance germane to evolutionary inference at the scale of landscape history. Interpretations of phylogeographic population structure at the interspecific level often grade into broader issues of species concepts and taxonomic assignments, so this concluding section also addresses these issues in greater detail. In particular, phylogeographic studies can be highly informative about population demography, geography, and temporal durations of the speciation process.
Chapter 5. Genealogical concordance
Aspect 1: Agreement across characters within a gene
Aspect 2: Agreement across genes
Aspect 3: Agreement across codistributed species
Aspect 4: Agreement with other biogeographic data
Regional perspectives: the southeastern United States
Environmental background
Terrestrial realm
Maritime realm
Genetic findings
Maritime species
Freshwater and terrestrial turtles
Other multispecies regional appraisals
Small mammals of lowland Amazonia
South american cats
Plants of the American Pacific Northwest
Marine organisms and the Trans-Arctic interchange
Vertebrates in fragmented Australian rainforests
Geminate marine taxa across the Isthumus of Panama
The Hawaiian volcanic conveyor belt
Additional examples
Genealogical discordance
Aspect 1: Disagreement across characters within a gene
Aspect 2: Disagreement across genes
Aspects 3 and 4
Concordance and phylogeographic depth
Conservation relevance of phylogeographic depth
Shallow separations: management units
Deep separations: evolutionarily significant units
Conservation issues in individual species
Conservation issues in regional biotas
Absolute times of phylogroup separation
Summary
Chapter 6. Speciation processes and extended genealogy
Phylogeography and the origin of species
The phylogenetics of speciation
Population or species-level phylogenies
Gene genealogies
Biological versus phylogenetic species concepts
A BSC/PSC reconciliation
Nomenclature
Species realities
Sexual taxa
Asexual taxa
Conclusions about the BSC/PSC debate
Speciation durations
Birds
Mammals
Other vertabrate groups
Deep phylogeography
Gene trees in anciest phylogenies
Phylogeography beyond the species level
Vicariance, dispersal, and arrival times
Phylogenetic character mapping of geography
Summary
Synopsis, and the future of phylogeography
Work cited
Index
