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Phylogenetics [Kietas viršelis]

(, Department of Mathematics and Statistics, University of Canterbury; Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand), (, Department of Mathematics and Statistics, University of Canterbury; Allan Wilson Centre for)
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The mathematical foundations of phylogenetics are Semple and Steel's (both mathematics and statistics, U. of Canterbury, New Zealand) main concern as they address a basic problem that has been of interest since Darwin first proposed the theory of evolution: how can the present characteristics of a group of species be used to infer, in their evolution from a common ancestor, the historical relationships between these species. The evolutionary or phylogenetic tree has been used to represent such relationships. Annotation (c) Book News, Inc., Portland, OR (booknews.com)

'Phylogenetics' is the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics. It is a flourishing area of interaction between mathematics, statistics, computer science and biology.
The main role of phylogenetic techniques lies in evolutionary biology, where it is used to infer historical relationships between species. However, the methods are also relevant to a diverse range of fields including epidemiology, ecology, medicine, as well as linguistics and cognitive psychology
This book is intended for biologists interested in the mathematical theory behind phylogenetic methods, and for mathematicians, statisticians, and computer scientists eager to learn about this emerging area of discrete mathematics.
'Phylogenetics' in the 24th volume in the Oxford Lecture Series in Mathematics and its Applications. This series contains short books suitable for graduate students and researchers who want a well-written account of mathematics that is fundamental to current to research. The series emphasises future directions of research and focuses on genuine applications of mathematics to finance, engineering and the physical and biological sciences.

Recenzijos

The authors' versatility in words, as well as in mathematics, makes reading this book altogether an enjoyable experience for the mathematically-inclined. * Systematic Biology * The authors state in the preface that their intention is to provide "a reasonably self-contained overview of an expanding field". In our opinion, they certainly succeed in meeting that goal. * Systematic Biology * All in all, this book should serve as an excellent mathematical introduction to phylogenetics for beginners and as a good reference for experts in the field. * Systematic Biology * Concisely and clearly written, Phylogenetics is a must-read for mathematicians or computer scientists who wish to do research in molecular phylogenetics, computational biology and bioinformatics. I hope the book will attract powerful mathematicians into this exciting area of research. * TRENDS in Ecology and Evolution * ... this book provides a concise and lucid summary of the mathematics literature related to phylogenetics. * TRENDS in Ecology and Evolution *

Preliminaries 1(5)
Graphs and their role in biology
5(11)
Graphs
5(2)
Trees and forests
7(2)
Intersection graphs
9(2)
Applications of graphs in biology
11(3)
Exercises
14(2)
X-trees and phylogenetic trees
16(27)
X-trees
16(2)
Rooted X-trees
18(4)
Ranked trees and the coalescent process
22(3)
Tree shapes
25(3)
Randomly generated trees
28(2)
Tree rearrangement operations
30(3)
Reticulate evolution and co-phylogeny
33(2)
Phylogenetic forests
35(5)
Exercises
40(3)
Trees and splits
43(22)
Splits-Equivalence Theorem
43(4)
A partial order on X-trees
47(1)
Compatibility of X-trees
48(1)
The splits metric
48(2)
Hierarchies, clusters, and splits
50(3)
Consensus trees
53(1)
Cyclic split systems and weak hierarchies
54(2)
The Buneman graph
56(7)
Exercises
63(2)
Compatibility of characters
65(19)
Characters and convexity
65(4)
Character compatibility (perfect phylogeny)
69(5)
Strongly compatible characters
74(1)
Complexity of determining character compatibility
74(1)
Maximum compatibility
75(1)
Generalized characters and directional constraints
76(2)
Defining an X-tree by characters
78(4)
Exercises
82(2)
Maximum parsimony
84(26)
Classical parsimony
84(5)
Optimization on a fixed tree
89(2)
Extensions of classical parsimony
91(4)
Maximum parsimony trees
95(3)
Networks of maximum parsimony trees
98(4)
Combinatorial statistics of parsimony
102(6)
Exercises
108(2)
Subtrees and supertrees
110(35)
Restricted subtrees
110(1)
Maximum agreement subtrees
111(1)
Compatibility of semi-labelled trees
112(6)
A reconstruction algorithm for rooted trees
118(3)
Complexity analysis
121(3)
Supertree methods
124(3)
Closure and correction operations
127(3)
Defining a tree by subtrees
130(4)
Phylogenetic patchworks
134(7)
Exercises
141(4)
Tree-based metrics
145(38)
Dissimilarity maps and tree metrics
145(4)
Ultrametrics
149(6)
Reconstruction methods
155(5)
Split decomposition theory
160(3)
Ordinal methods
163(3)
Group-valued, non-symmetric dissimilarities
166(8)
Perturbing tree metrics
174(6)
Exercises
180(3)
Markov models on trees
183(35)
Matrix algebra
183(2)
Markov processes on trees and graphs
185(2)
Phylogenetic models of character evolution
187(4)
Tree reconstruction for the general Markov process
191(3)
Stationary and reversible models
194(4)
The Hadamard representation
198(4)
The `Felsenstein zone'
202(2)
Rate variation across characters
204(2)
Model-based reconstruction methods
206(3)
Algebraic properties of Markov processes on trees
209(6)
Exercises
215(3)
References 218(13)
Commonly used symbols 231(4)
Index 235