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Introduction to Phylogenetic Networks

Table of Contents

Preface
Introduction
  1.1Introductory Examples
1.1.1Evolutionary network
1.1.2Data-display network
  1.2Biology and Phylogenetics
  1.3Biology and Bioinformatics
Phylogenetic analysis
  2.1A Model of Evolutionary History
  2.2The Logic of Phylogeny Reconstruction
  2.3The Practice of Phylogeny Reconstruction
  2.4Rooted versus Unrooted Trees
  2.5Introduction to Phylogenetic Networks
  2.6The Causes of Reticulation
  2.7More on Phylogenetic Networks
Data-Display Networks
  3.1Exploratory Data Analysis
  3.2Features and Limitations of Networks
  3.3Character-Display Networks
3.3.1Splits graphs
3.3.2Parsimony networks
3.3.3Other character-display networks
  3.4Tree-Display Networks
3.4.1Consensus and super-networks
3.4.2Comparison of character- and tree-display networks
  3.5Available Software
Evolutionary Networks
  4.1Evolutionary Analysis
  4.2Features and Limitations of Networks
4.2.1Graphing the networks
4.2.2Representing the networks
4.2.3Producing the networks
  4.3Cluster and Triplet Networks
4.3.1Cluster networks
4.3.2Triplet networks
  4.4Process-Based Networks
4.4.4Hybridization – trees
4.4.5Horizontal gene transfer (HGT) – reconciliation
4.4.3Recombination – characters
4.4.1Deep coalescence – the coalescent
4.4.2Duplication–loss
4.4.6Using data-display networks
4.4.7Other methods
4.4.8Some thoughts on how to construct an evolutionary network
  4.5Available Software
Concluding Remarks
  5.1Overview
  5.2Comparison
  5.3Hypothesis Testing
  5.4The Future
Appendix – Examples of Reticulation Causes
References
Glossary
Index


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Last updated Friday 30 December 2011 by


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