Neotropical Diversification: Patterns and Processes (Fascinating Life Sciences)

Acknowledgements
Contents
Chapter 1: Introduction
	1 Book Plan
	References
Part I: Neotropical Diversity and Diversification
	Chapter 2: Neotropical Diversification: Historical Overview and Conceptual Insights
		1 Introduction
		2 The Latitudinal Biodiversity Gradients
		3 The Neotropics
		4 Historical Outline
			4.1 The Beginnings
			4.2 Biogeographical Inferences
			4.3 The Inception of Paleoecology
			4.4 The Molecular Revolution
		5 Conceptual and Methodological Insights
			5.1 Paradigm Shifting
			5.2 Unwarranted Generalizations
			5.3 Taxonomic Resolution
			5.4 Pleistocene Diversification and Refugia
			5.5 Diversification Timing and Drivers
			5.6 Potential Solutions
		6 Future Directions
		7 Final Remarks
		References
	Chapter 3: Beyond Refugia: New Insights on Quaternary Climate Variation and the Evolution of Biotic Diversity in Tropical Sout...
		1 Introduction
		2 Climate Variability During the Quaternary
			2.1 Was Amazonia Drier During the Last Glacial Maximum (and Other Glacial Intervals of the Quaternary) Than It Is Today?
			2.2 Short-Term (Millennial) Extreme Precipitation Events: Were They Sufficient to Establish or Destroy Forested Habitat?
		3 Biological Responses to Quaternary Climate Variation
			3.1 Biome Expansions and Contractions in Response to Orbital and Millennial Climate Change: Was Pleistocene Climate Variabilit...
			3.2 Shifts in Community Composition Through Climate-Mediated Dispersal
			3.3 Perspectives on Climate, Topography, Soils, and Diversification in the Quaternary
		4 Conclusions
		References
	Chapter 4: Tropical and Subtropical South America: A Study of Community Turnover Across Environmental Gradients
		1 Introduction
		2 South America: General Descriptions of Geographical Landscape and Climate
		3 Biodiversity in South America
		4 Does the Tropical-Subtropical Environmental Transition Influence Community Composition in South America?
		References
	Chapter 5: Evolutionary Macroecology and the Geographical Patterns of Neotropical Diversification
		1 Introduction
		2 Mapping Phylogenetic History in Geographic Space
		3 Expanding the Community Phylogenetics Framework to Macroecology
		4 New Methods to Study Diversification at Macroecological Scales
		5 Perspectives and Concluding Remarks
		References
	Chapter 6: Evolutionary Imprints on Species Distribution Patterns Across the Neotropics
		1 Introduction
		2 Methods
			2.1 Data
			2.2 Phylogenetic Turnover
			2.3 Environmental and Biogeographic Predictors of Phylogenetic Turnover
		3 Results
		4 Discussion
		5 Concluding Remarks
		References
	Chapter 7: Diatom Diversity and Biogeography Across Tropical South America
		1 Introduction
		2 Lakes and Streams of Tropical South America: Natural Laboratories for the Study of Diatom Diversity and Ecology
		3 Effects of Local Environments, Climate, and Spatial Factors: Biogeography Meets Community Ecology
		4 Conclusions and Implications
		References
	Chapter 8: Avian Diversity in Humid Tropical and Subtropical South American Forests, with a Discussion About Their Related Cli...
		1 Introduction
		2 Target Forests in Tropical and Subtropical South America
			2.1 Amazonia
			2.2 The Pacific Forest
			2.3 The Forest of the Eastern Andean Slopes
			2.4 The Atlantic Forest
		3 Main Historical Processes Impacting Diversity in Tropical and Subtropical South America
			3.1 The Andean Uplift
			3.2 The Formation of the Isthmus of Panama
			3.3 Glaciations
			3.4 Sea-Level Rise
			3.5 Alternating Arid and Humid Periods
		4 Hypotheses to Explain Rainforest Biodiversity
		5 Present-Day Trends in Bird Diversity and Abundance in Tropical and Subtropical South America
		Appendices
			Appendix 1: Endemic Birds of the ``Pacific Slopes Center´´
			Appendix 2: Endemic Birds of the ``Atlantic Forest Mountains Center´´
			Appendix 3: Species that Would Have Been Involved in the Corridor Joining the Atlantic Forest with the Yungas
		Literature Cited
	Chapter 9: Contrasting Patterns of Temporal Diversification in Neotropical Butterflies: An Overview
		1 Introduction: The Neotropics as a Region and as a Group of Related Regions
		2 Rationale, Data Collection and Data Analyses
		3 Endemic (or Largely Endemic) Butterfly Clades, Including Supergeneric Radiations
			3.1 Tribe Ithomiini: 43 Genera, 354 spp. (Nymphalidae: Danainae)
			3.2 Tribes Brassolini + Morphini: 21 Genera, 137 spp. (Nymphalidae: Satyrinae)
			3.3 Tribe Haeterini: 5 Genera, 21 spp. (Nymphalidae: Satyrinae)
			3.4 Subtribe Euptychiina: 47 Genera, 391 spp. (Nymphalidae: Satyrinae)
			3.5 Subtribe Pronophilina: 64 Genera, 630 spp. (Nymphalidae: Satyrinae)
			3.6 Tribe Preponini: 3 Genera, 21 spp. (Nymphalidae: Charaxinae)
			3.7 Tribe Anaeini: 9 Genera, 88 spp. (Nymphalidae: Charaxinae)
			3.8 Subfamily Biblidinae: 32 Genera, 249 spp. (Nymphalidae)
			3.9 Subtribe Phyciodina: 21 Genera, 133 spp. (Nymphalidae: Nymphalinae)
			3.10 Tribe Heliconiini 10 Genera, 72 spp. (Nymphalidae: Heliconiinae)
			3.11 Eumaeini: 80 Genera, 1058 spp. (Lycaenidae: Theclinae)
			3.12 Family Riodinidae: 124 Genera, 1324 spp.
			3.13 Family Hesperiidae
		4 Endemic Generic Radiations Not Included in the Above
			4.1 Genus Catasticta, 96 spp. (Pieridae: Pierinae: Aporiina)
			4.2 Genus Calisto, 47 spp. (Nymphalidae: Satyrinae)
		5 Newcomers: Groups that Originated Outside the Neotropics
			5.1 Tribe Leptocircini: 4 Genera, 42 spp. (Papilionidae)
			5.2 Tribe Troidini: 3 Genera, 48 spp. (Papilionidae)
			5.3 Subfamily Dismorphiinae 6 Genera, 51 spp. (Pieridae)
			5.4 Genus Adelpha, Approx. 200 spp. (Nymphalidae: Limenitidinae)
			5.5 Genera Actinote, Altinote and Abananote, Approx. 50 spp. (Heliconiinae: Acraeini)
			5.6 Andean Polyommatini 7 Genera, 70 spp. (Lycaenidae)
		6 Discussion
			6.1 Drivers of Diversification in Butterflies
			6.2 Hostplants
			6.3 Age
			6.4 Rivers
			6.5 Pleistocene Refugia
			6.6 It Is Not About Rates
			6.7 Tempo and Mode of Speciation in the Neotropics-Substance or Semantics?
		7 Concluding Remarks
		References
Part II: Regional Biodiversity Patterns and Diversification Processes
	Chapter 10: The Origin and Evolution of Amazonian Species Diversity
		1 Introduction
		2 How Much Amazonian Diversity Do We Really Know?
		3 When Did the Modern Amazonian Biota Originate?
		4 Pliocene and Pleistocene Landscape Evolution: Implications for Diversification
		5 If the Amazonian Landscape Was Dynamic, How Did Biogeographic Patterns Arise?
		6 Building a Picture of the Diversification and Assembly of the Amazonian Biota
		References
	Chapter 11: Patterns and Processes of Diversification in Amazonian White Sand Ecosystems: Insights from Birds and Plants
		1 Introduction
		2 Origin and Evolution of White Sand Soils in Amazonia
		3 Species Assemblages in Amazonian WSE: Low Richness But High Endemism
			3.1 Plants
			3.2 Birds
		4 Phylogenetic Origin and Phylogeographic Patterns in Species Associated with WSE
			4.1 Plants
			4.2 Birds
		5 Conclusions and Perspectives
		References
	Chapter 12: On the Young Savannas in the Land of Ancient Forests
		1 Introduction
		2 Evolutionary Patterns of Extant Clades
		3 Inferences from the Fossil Record
		4 Climate Evolution and Savannas
		5 Origin, Assembly, and Expansion of Neotropical Savannas
		6 Advancing Knowledge on the Origin and Evolution of Savannas
		7 Conclusions
		References
	Chapter 13: Diversity, Endemism, and Evolutionary History of Montane Biotas Outside the Andean Region
		1 Introduction
		2 Non-Andean South American Mountains: What Are They?
		3 Non-Andean South American Mountains: What Lives There?
		4 Evolutionary Origins and Species Diversification in Non-Andean Mountains: Insights from Phylogenetic Studies
		5 Connecting Studies of Biodiversity and Human Impacts on Non-Andean Montane Biotas: A Case Study from the Serra Do Mar Range
		6 Future Directions
		References
	Chapter 14: Diversification in Ancient and Nutrient-Poor Neotropical Ecosystems: How Geological and Climatic Buffering Shaped ...
		1 Introduction
		2 Towards a Mechanistic Understanding of Ocbil Theory
			2.1 Driver-Pattern Feedbacks
			2.2 The Interplay Between Patterns and Mechanisms
		3 Plant Diversity and Endemism in Neotropical Ocbils: The Untold History of Ancient and Nutrient-Poor South American Vegetation
			3.1 Campos Rupestres
			3.2 Vegetation on Cangas
			3.3 Campos de Altitude
			3.4 Inselbergs
		4 Diversification and Population Genetics in Campos Rupestres
		5 Conclusions
			5.1 Areas of Future Research
		References
	Chapter 15: The Pantepui ``Lost World´´: Towards a Biogeographical, Ecological and Evolutionary Synthesis of a Pristine Neotro...
		1 Introduction
		2 Pantepui
			2.1 Physical Setting
			2.2 Climate
		3 Existing Knowledge
			3.1 Biogeography
				3.1.1 Phytogeography
				3.1.2 Zoogeography
				3.1.3 An Integrative View
			3.2 Ecology
				3.2.1 Present-Day Patterns
				3.2.2 Long-Term Processes
				3.2.3 Biogeographical Implications
			3.3 Evolution
				3.3.1 The Biogeographical Phase
				3.3.2 The Paleoecological Phase
				3.3.3 Molecular Phylogenetics and Phylogeography
			3.4 Conservation
				3.4.1 Direct Impacts
				3.4.2 Global Warming
		4 Future Research
			4.1 Biodiversity and Endemism
			4.2 Ecology and Paleoecology
			4.3 Genomics and Evolution
			4.4 Conservation
			4.5 Summary
		5 Conclusions
		References
	Chapter 16: Patterns of Species and Lineage Diversity in the Atlantic Rainforest of Brazil
		1 Introduction
		2 Spatial Patterns of Species Richness
		3 Large-Scale Community Turnover
		4 Areas of Endemism and Regionalization
			4.1 The Pernambuco Area of Endemism
			4.2 The Central Bahia Area of Endemism
			4.3 The Coastal Bahia Area of Endemism
			4.4 The Serra do Mar Area of Endemism
			4.5 The Paran/Araucaria Area of Endemism
		5 Phylogenetic Relationships Among Regional Biotas
			5.1 Intra-specific Patterns of Lineage Diversity
		6 Biogeographical Hypotheses
			6.1 Historical Connections Between the Atlantic Forest and Other Neotropical Biomes
			6.2 Regionalization Hypotheses
			6.3 Narrow-Scale Diversification and Microrefugia in Southern Atlantic Forest
		7 Implications for Conservation
		8 Conclusions and Future Prospects
		References
	Chapter 17: Forests Diversity in the Mexican Neotropics: A Paleoecological View
		1 Introduction
			1.1 The Mexican Neotropics
			1.2 Biodiversity in Mexico
			1.3 The Palaeoecological View in Long-Term Studies
			1.4 Records of Palaeodiversity in the Mexican Neotropics
			1.5 Palaeodiversity Measures
		2 Methods
		3 Results and Discussion
			3.1 Fossil Pollen Abundances in the Highlands
			3.2 Fossil Pollen Abundances in the Lowlands
			3.3 Holocene Diversity
		4 Conclusions
		References
	Chapter 18: Bioregions of Eastern Brazil, Based on Vascular Plant Occurrence Data
		1 Introduction
		2 Methods
		3 Results
		4 Discussion
		References
	Chapter 19: Human Contribution to Amazonian Plant Diversity: Legacy of Pre-Columbian Land Use in Modern Plant Communities
		1 Introduction
		2 Historical Scientific Background and Hypotheses
		3 The Debate Reactivated
			3.1 Broad-Scale Patterns
			3.2 Regional Patterns
				3.2.1 Eastern Amazonia: Coastal Regions of Amazonia and the Guiana Shield
				3.2.2 Central Amazonia
				3.2.3 South and Southwestern Amazonia
		4 Towards a Common View
		5 Final Remarks
		References
	Chapter 20: Historical Biogeography of Caribbean Plants Revises Regional Paleogeography
		1 Introduction
			1.1 The Caribbean Islands or West Indies
			1.2 A Paleogeographical Review of the Antilles
			1.3 Hypotheses that Explain the Origin of Caribbean Biota
			1.4 Time-for-Speciation Effect in the Caribbean
		2 Methods
		3 Results
		4 Discussion
		References
	Chapter 21: The Diversification of Extant Angiosperms in the South America Dry Diagonal
		1 Introduction
		2 Paleovegetation Reconstruction in the Dry Diagonal
		3 The State of the Art: A Scientometric View of Phylogeography in the Dry Diagonal
		4 The Role of Neogene Geological Events and Quaternary Climate Changes in Lineage Diversification in the Dry Diagonal
		5 Conclusion
		References
Part III: Taxon-Based Local and Regional Studies
	Chapter 22: Amphibians and Reptiles of Venezuelan Guayana: Diversity, Biogeography and Conservation
		1 Introduction
		2 The Venezuelan Guayana
		3 Herpetofauna of the Venezuelan Guayana
			3.1 State of Knowledge
			3.2 Richness and Endemism
				3.2.1 Altitudinal Shifts in Richness and Composition
			3.3 Distribution Patterns
				3.3.1 The Tepui Amphibians and Reptiles
		4 Conservation of the Herpetofauna of Venezuelan Guayana
		5 Final Remarks
		Appendix 1. Amphibians of the Venezuelan Guayana
		Appendix 2. Reptiles of the Venezuelan Guayana
		References
	Chapter 23: Origin of Elevational Replacements in a Clade of Nearly Flightless Birds: Most Diversity in Tropical Mountains Acc...
		1 Introduction
		2 Methods
		3 Results
		4 Discussion
		References
	Chapter 24: Clade-Specific Biogeographic History and Climatic Niche Shifts of the Southern Andean-Southern Brazilian Disjuncti...
		1 Introduction
		2 Material and Methods
		3 Results
		4 Discussion
		Appendix
		References
	Chapter 25: Biotic and Landscape Evolution in an Amazonian Contact Zone: Insights from the Herpetofauna of the Tapajós River B...
		1 Landscape Evolution in Amazonia and Its Signatures
		2 The Tapajós River Basin and Its Dual Role as a Barrier for the Biota
		3 The Tapajós River Basin´s Dynamic History
		4 Amphibians and Reptiles of the Tapajós River Basin
		5 Amphibian and Reptile Diversification Across Space and Time
		6 Landscape Evolution and Diversification at the Tapajós River Basin
		References
	Chapter 26: Diversification Processes in Lizards and Snakes from the Middle São Francisco River Dune Region, Brazil
		1 Introduction
		2 Characterization of the Dune Fields
		3 Diversity and Distribution of the Squamate Fauna
		4 Phylogenetic Patterns
		5 Geographic Structure within Species
		6 Conclusions
		Appendix 1: Updated list of Squamate Reptiles Occurring on the Middle São Francisco Dune Region
		Appendix 2: Description of Methods Implemented for Molecular Analysis
			Bayesian Phylogeny and Estimates of Divergence Times
			Genetic Distances
			Statistical Test of Genetic Structure
		References
	Chapter 27: Unexpected Beta-Diversity Radiations in Highland Clades of Andean Terraranae Frogs
		1 Introduction
		2 Historical Account and the State of the Art
		3 Morphological Diversity and Ecological Correlates
		4 Life History Variation
		5 Genetics, Biogeographical Patterns, and Species Diversity: Why So Many Species?
		6 Future Research and Conservation
		References
	Chapter 28: Disparate Patterns of Diversification Within Liolaemini Lizards
		1 Introduction
		2 Materials and Methods
			2.1 DNA Sequences
			2.2 Time-Calibrated Phylogenetic Tree
			2.3 Net Diversification, Speciation and Extinction Rates
			2.4 Body Size Evolution
			2.5 Statistical Comparisons
		3 Results
			3.1 Liolaemini Phylogenetic Relationships
			3.2 Net Diversification, Speciation and Extinction Rates
			3.3 Body Size Evolution
			3.4 Link Between Diversification Rates and Body Size Evolution Rates
		4 Discussion
			4.1 Disparate Patterns of Diversification in Liolaemini Lizards
			4.2 The Link Between Body Size Evolution and Diversification
			4.3 Implications for Conservation
		References
	Chapter 29: Diversification History of Neotropical Lecythidaceae, an Ecologically Dominant Tree Family of Amazon Rain Forest
		1 Introduction
		2 Methods
			2.1 Tree Building
			2.2 Ancestral Range Reconstruction
			2.3 Diversification Analyses
		3 Results
		4 Discussion
			4.1 Systematics of Lecythidoideae
			4.2 Spatiotemporal Patterns in the Lecythidoideae
				4.2.1 Dispersal of Lecythidaceae to the New World
				4.2.2 Diversification Within the Neotropics
			4.3 Diversification Rates
			4.4 Caveats of Our Study
			4.5 Conclusions and Future Directions
		References
Part IV: Epilogue
	Chapter 30: Conservation in the Neotropics: A Final Reflection
		References
Correction to: Neotropical Diversification: Patterns and Processes
	Correction to: V. Rull, A. C. Carnaval (eds.), Neotropical Diversification: Patterns and Processes, Fascinating Life Sciences ...