Phylogeography : Concepts, Intraspecific Patterns and Speciation Processes.

Intro -- Genetics - Research and Issues -- Library of Congress Cataloging-in-Publication Data -- Contents -- Preface -- Phylogeography and Speciation Processes in Marine Fishes and Fishes from Large Freshwater Lakes -- Abstract -- Phylogeography of Fishes in Large Water Bodies -- The (Phylo-)Geography of Speciation -- Marine versus Lacustrine Adaptive Radiations in Fishes -- The Geographic Scale of Gene Flow in Fishes -- Lacustrine Fishes -- Riverine and Anadromous Fishes -- Marine Fishes -- Three Adaptively Radiating Perciform Groups -- Phylogeography and Speciation in Marine Versus Lacustrine Fishes -- Conclusion -- Acknowledgments -- References -- Phylogeography: its Importance in Insect Pest Control -- 1. Summary -- 2.The Problem -- 3. The Challenge -- 4. The Tools: Biogeography and Molecular Genetics -- 5. Specific Questions -- 6. Bioinvasions: Whiteflies in the Canary Islands -- 7. Colonisation Patterns: The Iberian Peninsula in the Expansion History of the Medfly -- 8. Population Structure: The Olive Fly in the Mediterranean Basin -- 9. Conclusion -- References -- Host Specificity and Speciation in Parasitic Plants -- Abstract -- Parasitic Plants -- The Search for Photosynthetic Ancestors -- Keystone Species and Ecosystem Engineers -- Host Specificity -- Host Specificity as a Promoter of Speciation -- Host-Driven Speciation in Hemiparasitic Plants -- Host-Driven Speciation in Holoparasitic Plants -- Conclusion -- References -- Gene Flow, Genetic Drift, and Geographic Variation of the Ainu: An Assessment Based on Nonmetric Cranial Traits -- Abstract -- Introduction -- Materials and Methods -- Results -- Discussion -- Acknowledgments -- References -- Suture Zones and Phylogeographic Concordance: Are They the Same and How Should We Test for Their Existence? -- Abstract -- The Suture Zone Concept and Phylogeographic Concordance.

Previous Tests for the Existence of Suture Zones -- A New Stastical Framework for Detecting the Existence of Suture Zones and Phylogeographic Concordance -- Conclusion -- Acknowledgments -- References -- Differentiation History of Dragonflies in the Insular East Asia Revealed by the Gene Genealogy (Odonata: Hexapoda) -- Abstract -- Introduction -- Case I-Differentiation Process of the Genus Davidius in the Insular East Asia -- Ecological Differentiation -- Timing of Divergence Inferred From COI Sequence Data -- Case II-Divergence History of Anotogaster sieboldii (Selys, 1854) -- Subdivided Ppulations -- Differentiation Hstory of A. sieboldii -- Interesting Patterns of Distribution in the Insular East Asia -- Case I-Isolated Distribution wth Facing Each Other Across Closely Related Species -- Case II-Living Fossil Dragonfly -- Conclusion -- References -- Statistical Phylogeography, Ecological Niche Models and Predicting Glacial Refugia: An Examination of Key Assumptions -- Abstract -- Ecological Niche Models and Phylogeography -- Assumptions and Reason for Concern -- Assumption 1: The Abiotic Control Assumption -- Assumption 2: Communities Are Closed Systems Through Space and Time -- Assumption 3: Historical Climate Data are Accurate and Non-Analog Climates are Unimportant -- Assumption 4: Landmass Dynamics Are Known or Static -- Assumption 5: Critical Abiotic Variables are Known -- Conclusion -- Acknowledgments -- References -- The Need for a Multispecies, Multilocus Phylogeographical Approach -- Introduction -- Single vs Multiple Loci Issue -- The Importance of Geography -- Synthesis -- References -- Phylogeography of Finches and Sparrows -- Abstract -- Introduction -- Parallel Fringillidae and Passeridae Evolutive Radiations -- A. Old World Sparrows (fam. Passeridae, sfam. Passerinae, gen. Passer).

1. Main conclusions about the genetic relatedness among old world sparrows and others -- Origin and Other Comments about Genus Passer -- P. melanurus -- The P. hispaniolensis italiae Classification -- 2. Relationships of Old World Sparrows with Other Genera -- B. Estrildinae Finches (fam. Passeridae, sfam. Estrildinae) -- 1. Tempo of evolution and origin in the indian subcontinent -- 2. Specific phylogenetic problems addressed -- Genera Estrilda and Nesocharis -- Gouldian Finch -- Silverbills -- Java Sparrow (Padda oryzivora / Lonchura oryzivora) -- African Munias -- Plum-headed Finch (Aidemosyne modesta / Neochmia modesta) -- Red-browed Firetail (Aegintha / Neochmia temporalis) -- Cryptospiza Radiation -- C. Carduelini Finches (fam. Fringillidae, sfam. Fringillinae, tribe Carduelini) -- 1. Genus Carduelis -- Eurasian Goldfinch (Carduelis carduelis) and Citril Finch (Carduelis citrinella) -- a. European Citril Finch: Islands and Continent -- b. Greenfinches (C. chloris, C. sinica, C. ambigua and C. spinoides) -- c. Desert Finch -- Biogeographic (Global Warming) Hypothesis -- Evolutionary Pattern Hypothesis -- Twite (Carduelis flavirostris) and Linnet (Carduelis cannabina): Related to American Goldfinches? -- North American Carduelis Radiations -- a. North American Goldfinch (Carduelis tristis) Radiation: Relationship with Twite and Linnet (Figures 10, 15) -- b. North American Pine Siskin (Carduelis pinus) Radiation: an Eurasian Ancestor Siskin, Carduelis spinus -- c. North / South American Siskin Radiation: a North American Ancestor, Carduelis notata -- Northern Redpolls (Carduelis flammea and Carduelis hornemanni): Disappearance of Genus Acanthis and Relationship with Crossbills (genus Loxia) -- 2. Genus Serinus: Radiations Intermingled in Time with those of Genus Carduelis.

Large African Canaries: Yellow Canary (S. Flaviventris), Brimstone Canary (S. Sulphuratus), Streaky-Headed Seedeater (S. Gularis), White-Throated Canary (S. Albogularis) -- African-Asian Canaries: Black-Headed Canary (S. Alario), Cape Canary (S. Canicollis), Fire-Fronted Serin (S. Pusillus), Syrian Finch (S. Syriacus) [31] -- Mediterranean Canaries: Wild and Domestic Island Canary (S. Canaria), European Serin (S. Serinus) -- Other Canaries: Oriole Finch (Linurgus Olivaceus) and Other Relict Serinus (S. Totta, S. Thibetanus, S. Striolatus) [17,25,31] -- Convergent Evolution -- 3. Sheading Different and Split Rosefinches (genus carpodacus) Radiations -- American "Carpodacus" finches (C. mexicanus, C. cassinii) -- Haematospiza sipahi / Carpodacus erythrinus roseatus -- Uragus sibiricus / Carpodacus rubicilloides -- Carpodacus pulcherrimus Radiation -- 4. Grosbeak Radiation -- 5. Bullfinches (Genus Pyrrhula) and their Ancestor, the Pine Grosbeak (Pinicola enucleator) -- 6. 'Arid-zone' Finches -- 7. Non-extant genus rhodopechys -- Conclusion -- 1. Genus Passer (Old World Sparrows) -- 2. Estrildinae Finches -- 3. Tribe Cardinalini -- 4. Tribe Carduelini -- Genus Carduelis (Goldfinches and Siskins) -- Genus Serinus (Canaries). Several Clades have been Observed: -- Acknowledgments -- References -- Appendix. Methodology -- A. Field Work -- B. Sampling and Sequencing -- C. Cyt-b -- D. Phylogenetic Methods -- 1. Cladistic Methods -- Maximum Parsimony Tree -- 2. Quantitative Methods -- Unweighted Pair Group with Arithmetic Mean (UPGMA) -- Neighbor Joining (NJ) -- Maximum Likelihood (ML) -- Bayesian Inference -- 3. Linearized Trees -- Index.

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