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Table of Contents
Intro
Preface
Acknowledgements
Contents
Part I: Introduction
Chapter 1: A Fresh Look at Conservation Genetics in the Neotropics
1.1 Introduction
1.2 Conservation Genetics at the Species Level
1.3 Genetics for Studying Communities and Ecosystems
1.3.1 Phylogenetic Diversity
1.3.2 Comparative Phylogeography
1.3.3 Environmental DNA and Invertebrate-Derived DNA and Conservation
1.4 Conservation Genomics in Neotropics
1.5 Final Considerations
References
Part II: Species and Conservation
Chapter 2: DNA Barcoding for Assessing Biodiversity
2.1 Introduction
2.2 DNA Barcoding, a Tool for Biological Identification
2.2.1 Molecular Markers
2.2.2 The Distance Approach and the DNA Barcoding Gap
2.2.3 Worldwide Initiatives
2.3 DNA Barcoding Methodologies
2.3.1 BOLD System
2.3.2 Voucher and Collection Data
2.3.3 Biological Preservation Methods
2.3.4 DNA Extraction Methods
2.3.5 PCR and Primers Commonly Used
2.3.6 Uploading Data to BOLD
2.4 Single-Gene Species Delimitation Methods
2.4.1 Molecular Operational Taxonomic Units
2.4.2 Distance vs Coalescent Species Delimitation Approaches
2.4.3 Barcode Index Number
2.4.4 Comparing Methods
2.5 DNA Barcoding in Neotropics
2.5.1 Using DNA Barcoding to Assess Biodiversity in Birds
2.5.2 Using DNA Barcoding to Assess Fish Biodiversity
2.5.3 Using DNA Barcoding to Assess Biodiversity in Marine Realm
2.5.4 Using DNA Barcoding to Assess Biodiversity in Insects
2.5.5 Using DNA Barcoding to Assess Biodiversity in Plants
2.6 Final Considerations
References
Chapter 3: Genetic Tools for the Conservation of Bats
3.1 Introduction
3.2 Literature Review of Genetic Techniques Applied in Bat Conservation
3.3 Issues and Timeline Overview
3.4 Molecular Identification and Taxonomy
3.5 Demographic History, Biogeography, Life History and Genetic Diversity
3.6 Lessons from Population Genetics
3.6.1 Impacts of Geographical Barriers and Distance on Gene Flow
3.6.2 Genetic Structure of Populations
3.6.3 Bats in Islands
3.6.4 Effect of Fragmentation and Other Anthropogenic Effects on Genetic Diversity
3.6.5 Bat Adaptations
3.7 Final Considerations
References
Chapter 4: Status Quo and Orchid Conservation Challenges in the Neotropical Region
4.1 Introduction
4.2 Genetic Conservation in Orchidaceae
4.3 Neotropical Orchids
4.4 Phylogenetic Relationships
4.5 Population Genetics
4.6 Final Considerations
References
Chapter 5: Population Differentiation with Introgression
5.1 Introduction
5.2 Population Differentiation and Speciation Genomics
5.3 Balance of Gene Flow and Drift Shape Population Structure
5.4 Population Structure and Secondary Contact
5.5 Patterns of Introgression Across the Genome
5.6 Balance Between Gene Flow and Selection and Population Structure
5.7 Anthropogenic Impact on Introgression
Preface
Acknowledgements
Contents
Part I: Introduction
Chapter 1: A Fresh Look at Conservation Genetics in the Neotropics
1.1 Introduction
1.2 Conservation Genetics at the Species Level
1.3 Genetics for Studying Communities and Ecosystems
1.3.1 Phylogenetic Diversity
1.3.2 Comparative Phylogeography
1.3.3 Environmental DNA and Invertebrate-Derived DNA and Conservation
1.4 Conservation Genomics in Neotropics
1.5 Final Considerations
References
Part II: Species and Conservation
Chapter 2: DNA Barcoding for Assessing Biodiversity
2.1 Introduction
2.2 DNA Barcoding, a Tool for Biological Identification
2.2.1 Molecular Markers
2.2.2 The Distance Approach and the DNA Barcoding Gap
2.2.3 Worldwide Initiatives
2.3 DNA Barcoding Methodologies
2.3.1 BOLD System
2.3.2 Voucher and Collection Data
2.3.3 Biological Preservation Methods
2.3.4 DNA Extraction Methods
2.3.5 PCR and Primers Commonly Used
2.3.6 Uploading Data to BOLD
2.4 Single-Gene Species Delimitation Methods
2.4.1 Molecular Operational Taxonomic Units
2.4.2 Distance vs Coalescent Species Delimitation Approaches
2.4.3 Barcode Index Number
2.4.4 Comparing Methods
2.5 DNA Barcoding in Neotropics
2.5.1 Using DNA Barcoding to Assess Biodiversity in Birds
2.5.2 Using DNA Barcoding to Assess Fish Biodiversity
2.5.3 Using DNA Barcoding to Assess Biodiversity in Marine Realm
2.5.4 Using DNA Barcoding to Assess Biodiversity in Insects
2.5.5 Using DNA Barcoding to Assess Biodiversity in Plants
2.6 Final Considerations
References
Chapter 3: Genetic Tools for the Conservation of Bats
3.1 Introduction
3.2 Literature Review of Genetic Techniques Applied in Bat Conservation
3.3 Issues and Timeline Overview
3.4 Molecular Identification and Taxonomy
3.5 Demographic History, Biogeography, Life History and Genetic Diversity
3.6 Lessons from Population Genetics
3.6.1 Impacts of Geographical Barriers and Distance on Gene Flow
3.6.2 Genetic Structure of Populations
3.6.3 Bats in Islands
3.6.4 Effect of Fragmentation and Other Anthropogenic Effects on Genetic Diversity
3.6.5 Bat Adaptations
3.7 Final Considerations
References
Chapter 4: Status Quo and Orchid Conservation Challenges in the Neotropical Region
4.1 Introduction
4.2 Genetic Conservation in Orchidaceae
4.3 Neotropical Orchids
4.4 Phylogenetic Relationships
4.5 Population Genetics
4.6 Final Considerations
References
Chapter 5: Population Differentiation with Introgression
5.1 Introduction
5.2 Population Differentiation and Speciation Genomics
5.3 Balance of Gene Flow and Drift Shape Population Structure
5.4 Population Structure and Secondary Contact
5.5 Patterns of Introgression Across the Genome
5.6 Balance Between Gene Flow and Selection and Population Structure
5.7 Anthropogenic Impact on Introgression