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Tree Balance Indices: A Comprehensive Survey

✍ Scribed by Mareike Fischer, Lina Herbst, Sophie Kersting, Annemarie Luise Kühn, Kristina Wicke


Publisher
Springer
Year
2023
Tongue
English
Leaves
398
Edition
1
Category
Library

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✦ Synopsis


Whether you are looking for an introduction to the field of tree balance, a reference work on the multitude of available balance indices or inspiration for your future research, this book offers all three. It delves into the significance of tree balance in phylogenetics and other research domains, where numerous indices have been introduced over the years. While the variations in definitions and underlying principles among these indices have long remained a challenge, this survey addresses the problem by presenting formal definitions of balance and imbalance indices and establishing desirable properties.

The book is comprehensive both in the inclusion of a variety of indices and in the information provided on them: the authors meticulously analyze and categorize established indices, shedding light on their general, statistical and combinatorial properties. They reveal that, while some known balance indices fail to meet the most basic criteria, certain tree shape statistics from other contexts prove to be effective balance measures. The collected properties are neatly presented, numerous new results are established, open research questions are highlighted, and possible applications are discussed.

Reviewing over twenty (im)balance indices, a wealth of mathematical insights is provided, accompanied by real-world examples showcasing the importance of tree balance in diverse research areas. Catering to researchers, students, mathematicians, and biologists, the book can be used as a textbook for university seminars, a reference on tree balance, and as a source of inspiration for future research. It is accompanied by the free R package 'treebalance', a powerful tool to further explore and apply the discussed concepts, and a website allowing quick access to the main information and the latest developments in the field.

✦ Table of Contents


Forewords
Foreword by Professor Mike Steel (University of Canterbury)
Foreword by Professor Arne Mooers (Simon Fraser University)
Preface
Acknowledgements
Contents
Part I Introduction
Chapter 1 Opening remarks
Organization of this book.
Using this book as a reference guide.
Using this book as a textbook for a university seminar.
Chapter 2 Preliminaries
2.1 General notation and concepts
2.2 Rooted trees and related concepts
Rooted (binary) trees.
Ancestors, descendants, and cherries.
Depth, height, and width.
Cophenetic value and nodal distance.
Pending subtrees and decomposition of rooted trees.
Rooted quartets.
Symmetry nodes, balance values, and 𝐼𝑣 values.
Special trees.
2.3 Ordering and enumerating rooted (binary) trees
Furnas ranking scheme.
Number of rooted (binary) trees.
2.4 Probabilistic models of phylogenetic trees
Phylogenetic trees.
The Aldous’ 𝛽-splitting model of binary phylogenetic trees.
The Yule model – a special case of Aldous’ 𝛽-splitting model.
The uniform model – a special case of Aldous’ 𝛽-splitting model.
Chapter 3 A brief sketch on the relevance and history of tree balance
The relevance and history of tree balance and related concepts in evolutionary biology.
Probabilistic models for phylogenetic trees and their link to tree balance.
Discriminating the evolutionary dynamics of RNA viruses by means of tree balance.
Chapter 4 Concepts of tree balance and imbalance
4.1 Definition of tree balance and imbalance
Less established tree shape statistics that are (im)balance indices.
4.2 General, combinatorial and statistical properties
Part II Tree balance and imbalance indices
Chapter 5 Sackin index
Chapter 6 Average leaf depth
Chapter 7 Variance of leaf depths
Chapter 8 Total cophenetic index
Chapter 9 ŝ-shape statistic
Chapter 10 B1 index
Chapter 11 B2 index
Chapter 12 Colless index
Chapter 13 Corrected Colless index
Chapter 14 Corrected Colless index / I2 index
Chapter 15 Quadratic Colless index
Chapter 16 Colless-like indices
Chapter 17 I-based indices
Chapter 18 Symmetry nodes index
Chapter 19 Rogers J index
Chapter 20 Rooted quartet index
Chapter 21 ColΔ³n-Plazzotta rank
Chapter 22 Furnas rank
Chapter 23 Less established tree shape statistics that are (im)balance indices
23.1 Total internal path length
23.2 Total path length
23.3 Average (vertex) depth
23.4 Maximum depth
23.5 Maximum width
23.6 Modified maximum difference in widths
23.7 Maximum width over maximum depth
23.8 stairs1
23.9 stairs2
Chapter 24 Related tree shape statistics that are not (im)balance indices
24.1 Diameter, area per pair index, and the Wiener index
24.2 Farness and betweenness centrality
24.3 Degree of root imbalance, I value, and the mean I'10 index
24.4 D index
24.5 Maximum difference in widths
24.6 Cherry index and modified cherry index
24.7 ILnumber and ladder length
24.8 Number of pitchforks, double cherries, 4-caterpillars and clades of size x
Chapter 25 Extension of tree balance and imbalance indices and alternative ways of measuring tree balance
25.1 Obtaining new balance indices from established indices
25.2 Normalizing (im)balance indices
25.3 Alternative ways of measuring tree balance
Part III Applications and outlook
Chapter 26 Software
26.1 Existing software packages
26.2 The software package treebalance
26.3 Examples for the usage of treebalanceof
26.3.1 Implementing the uniform model based on the Furnas rank and the symmetry nodes index
26.3.2 Uncovering divergence from expected imbalance
26.3.3 Exploring the range and number of distinct (im)balance index values
Chapter 27 Applications
Using the mean Iβ€²' index to detect fertility inheritance.
Measuring diversity skewness with the corrected Colless index.
(Im)balance of disease outbreak trees.
The influence of allopatry on the Sackin index.
Using the Iwv values to uncover the variation in language diversification and extinction rates.
The influence of different symmetric division rates on the balance of simulated tumor progression phylogenies.
Chapter 28 Discussion and outlook
28.1 Summary and discussion
28.2 Directions for future research
Appendix A Lookup Tables
References
List of symbols
General mathematical notation
General notation for rooted (binary) trees
Vertex properties
Tree properties
Subtrees, decompositions, and restrictions
Special trees
Phylogenetic trees
Probabilistic models of phylogenetic trees
Concepts of tree balance and imbalance
Other tree shape statistics
Index

✦ Subjects


Phylogenetics; Tree Balance; Yule Model; Search Trees; Colless Index; Sackin Index; Total Cophenetic Index; Uniform Model


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