Biodiversity and Biogeographic Patterns in Asia-Pacific Region I: Statistical Methods and Case Studies

Table of Contents

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FOREWORD

PREFACE

ACKNOWLEDGEMENTS

CONFLICT OF INTEREST

Species Richness and Diversity

Abstract

INTRODUCTION

MEASURE OF SPECIES DIVERSITY

Species Richness

Shannon Diversity Index

Simpson Diversity Index

Renyi Entropy

EXTRAPOLATION OF SPECIES RICHNESS

Chao1 and Chao2 Indices

Jackknife Estimators

Rarefaction Curve

REMARKS

REFERENCES

Functional Diversity

Abstract

INTRODUCTION

Different Functional Diversity Indices

Originality of Functional Diversity

Uniqueness of Functional Diversity

Quadratic Entropy

Functional Divergence [7]

Functional Regularity [8]

Functional Attribute Diversity [9]

Functional Richness in One Dimension [10]

Functional Evenness (FE) in One Dimension [10, 11]

Functional Evenness (FE) in Multiple Dimensions [10, 11]

Functional Distance (FDIS) [13]

REMARKS

REFERENCES

Phylogenetic Diversity

Abstract

INTRODUCTION

MEASURE OF PHYLOGENETIC DIVERSITY BY NODE-BASED METHODS

MEASURE OF PHYLOGENETIC DIVERSITY BY BRANCH-BASED METHODS

Total Phylogenetic Diversity

Pendant Edge

Taxonomic Distinctiveness

Evolutionary Distinctiveness

Phylogenetic Endemism Index (PE)

Phylogenetic Ancestral Range Index

Imperiled Phylogenetic Diversity Index (IPD Index)

REMARKS

REFERENCES

Multiple-Site Beta Diversity Methods with an Introduction of R Package MBI

Abstract

INTRODUCTION

Empirical Evaluation of the Multiple-Site Beta Diversity Indices

RESULTS AND DISCUSSION

A Comparison of All Multiple-Site Indices

REFERENCES

Species-Site Compositional Matrix Comparison Methods

Abstract

INTRODUCTION

STATISTICAL METHODS FOR MATRIX COMPARISON

Mantel Test

Mantel Correlogram

Partial Mantel Correlogram

Multiscale Mantel Correlogram

Procrustes Analysis

Partial Procrustes Correlogram

Multiscale Procrustes Correlogram

Test of Significance Using Permutation Techniques

Test of Significance Using Fisher’s Z-Transformation Method

A PRACTICAL EXAMPLE USING BIRD AND MAMMAL DISTRIBUTION IN HAINAN ISLAND OF CHINA

Data Set

RESULTS

Distributional Concordance of Birds and Mammals

Multiscale Distributional Concordance Using (Partial) Mantel Correlogram

Multiscale Distributional Concordance Using (Partial) Procrustes Correlogram

DISCUSSION

REFERENCES

Ecological Ordination Methods-Principal Component Analysis, Principal Coordinate Analysis, Redundancy Analysis and Canonical Correspondence Analysis

Abstract

INTRODUCTION

PRINCIPAL COMPONENT ANALYSIS (PCA)

PRINCIPAL COORDINATE ANALYSIS (PCoA)

CANONICAL CORRESPONDENCE ANALYSIS (CCA)

REDUNDANCY ANALYSIS (RDA)

IMPLICATIONS

REFERENCES

Variation Partitioning Techniques

Abstract

INTRODUCTION

VARIATION PARTITIONING ON SPECIES COMPOSITION MATRIX

VARIATION PARTITIONING ON BETA DIVERSITY WITH NULL MODEL

Measurement of Beta Diversity

REMARKS

REFERENCES

Species Abundance Distribution

Abstract

INTRODUCTION

INTRODUCING SOME SAD MODELS

Zipf Model

Broken Stick Model (BSM)

Niche Preemption Model (NPM)

Geometric Model (GEOM)

Neutral Model (NM)

MODEL COMPARISON AND EVALUATION

A PRACTICAL EXAMPLE

Sampling Locations

SAD for Microarthropod Species as a Whole

SAD for Oribatids

SAD for Mesostigmatids

SAD for Collembolans

DISCUSSION

REFERNECES

Species-Area, Commonness-Area, Rarity-Area and Endemic Species-Area Relationships

Abstract

INTRODUCTION

MATERIALS AND METHODS

Species-Area Relationship (SAR)

Common Species-Area Relationship (CAR)

Rare Species-Area Relationship (RAR)

Endemic Species-Area Relationship (EAR)

Numerical Simulations

RESULTS

Overview of SAR, CAR, RAR, and EAR Curves

Influence of Aggregation Patterns of Species on SAR, CAR, RAR, and EAR

Influence of Species Abundance on SAR, CAR, RAR and EAR

DSICUSSION

REFERENCES

Statistical Methods for Estimating Species Abundance

Abstract

INTRODUCTION

RANDOM SAMPLING ALGORITHM (RS)

ADAPTIVE CLUSTER SAMPLING ALGORITHM (ACS)

A PRACTICAL EXAMPLE

RESULTS AND DIsCUSSION

REFERENCES

Testing Distributional Randomness

Abstract

INTRODUCTION

Quadrat-Based Method-Measurement of Distributional Aggregation of Species

Spatial Point-Based Method-Measurement of Distributional Aggregation of Species

REMARKS

REFERENCES

Modeling Species’ Potential Distribution

Abstract

INTRODUCTION

STATISTICAL ALGORITHMS

GARP

MAXENT

BIOCLIM

Ecological-Niche Factor Analysis (ENFA)

A PRACTICAL EXAMPLE

Suitable Range Prediction of the Haplotypes of Chrysanthemum Indicum in China Using Ecological Niche Modeling [14]

Distribution and Haplotype Information

Spatial and Environmental Variables

Model Configuration

Results and Discussion

REFERENCES

Phylogenetic Relatedness Pattern and Climatic Correlates on the Distribution of Endemic Birds in China

Abstract

INTRODUCTION

MATERIALS AND METHODS

Construction of Phylogenetic Tree and Distribution of Endemic Birds in China

Measurement of Phylogenetic Relatedness

Climatic Correlates of Phylogenetic Community Structure

RESULTS

Endemic Birds of China Showed Phylogenetic Overdispersion Pattern

Important Environmental Variables that May Influence the Phylogenetic Community Structure

DISCUSSION

REFERENCES

Quantifying the Relative Contribution of Climatic Variability and Dispersal Limitation on the Distribution of Endemic Birds of Mainland China Using Spatial Point Pattern Analysis

Abstract

INTRODUCTION

MATERIALS AND METHODS

Distribution of Endemic Birds of China

Variables Indicating Climatic Fluctuation

Variables Representing Dispersal Limitation

Spatial Point Analysis

RESULTS

DISCUSSION

REFERENCES

A Phylogenetic Ancestral Endemism Index (PAE) Incorporating the Information of Ancestral Ranges for Setting Conservation Priority of Species and Areas

Abstract

INTRODUCTION

MATERIALS AND METHODS

Phylogenetic Endemism Index

A Problem in Phylogenetic Endemism Index

A New Index Incorporating Ancestral Ranges of Extinct Lineages in Internal Nodes

A Practical Example

RESULTS

DISCUSSION

REFERENCES

Can Higher Taxonomic Hierarchy Units be Effective Surrogates of Plant Hotspots and Conservation Areas? A Test on Endemic Plants in a Tropical Biodiversity Hotspot

Abstract

INTRODUCTION

MATERIALS AND METHODS

Data Sets

Methods

Richness Mapping and Spatial Correlation

Conservation Priority Selection

RESULTS

Richness Mapping

Complementary Priority Areas

DISCUSSION

REFERENCES

Spatial Risk Assessment of Alien Plants in China Using Biodiversity Resistance Theory

Abstract

INTRODUCTION

MATERIALS AND METHODS

Invasive Plant Diversity Data

Woody Plant Diversity Data

Risk Mapping Using Empirical Bayes Smoothing and Poisson-Gamma Model

RESULTS AND DISCUSSION

REFERENCES

Biodiversity and Biogeographic Patterns

in Asia-Pacific Region I: Statistical

Methods and Case Studies

Authored By

Youhua Chen

Department of Renewable Resources

University of Alberta

Edmonton

T6G 2H1

Canada

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FOREWORD

Juan J. Morrone

Museo de Zoología ‘Alfonso L. Herrera’

Departamento de Biología Evolutiva

Facultad de Ciencias

Universidad Nacional Autónoma de México (UNAM)

Apartado Postal 70-399, 04510 Mexico D.F., Mexico

Biogeography is the biological discipline that studies the geographic distribution of plant and animal taxa and their attributes in space and time. Nowadays, it is passing through a revolution concerning its foundations, basic concepts, and methods. As part of this revolution, biogeographers are increasingly recognizing the need of integration with other disciplines, in order to develop a truly interdisciplinary and pluralist science. The recent discipline of conservation biogeography shows clearly the possibilities of interdisciplinary collaboration. Additionally, during the last decades, there has been a considerable progress in the quantitative analysis of biogeographical patterns, with statistical multivariate and phylogenetic methods proposed to analyse particular ecological and biogeographical patterns and to establish meaningful comparisons.

The book written by Youhua Chen presents a thoughtful analysis of different biogeographical methods and their application to the analysis of biotic patterns in the Asia-Pacific region, which encompasses China, India and southeast Asia, and represents a very interesting region, which possesses an outstanding biodiversity. The analyses of different plant and animal taxa, using several biogeographical methods, led Youhua to identify clear patterns and to correlate them with climatic and biological data. Finally, he highlighted the relevance of these patterns for biodiversity conservation.

There are different reasons to read this book. Biogeographers will be interested in an outstanding region of the world, with specific chapters on birds and plants as case studies. Conservationists will appreciate the identified biogeographical patterns, which might help them establish conservation