โ Scribed by Gusfield, Dan
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Combinatorial structure and algorithms for deducing genetic recombination history, represented by ancestral recombination graphs and other networks, and their role in the emerging field of phylogenetic networks.
In this book, Dan Gusfield examines combinatorial algorithms to construct genealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs). The algorithms produce networks (or information about networks) that serve as hypotheses about the true genealogical history of observed biological sequences and can be applied to practical biological problems.
Phylogenetic trees have been the traditional means to represent evolutionary history, but there is a growing realization that networks rather than trees are often needed, most notably for recent human history. This has led to the development of ARGs in population genetics and, more broadly, to phylogenetic networks. ReCombinatorics offers an in-depth, rigorous examination of current research on the combinatorial, graph-theoretic structure of ARGs and explicit phylogenetic networks, and algorithms to reconstruct or deduce information about those networks.
ReCombinatorics, a groundbreaking contribution to the emerging field of phylogenetic networks, connects and unifies topics in population genetics and phylogenetics that have traditionally been discussed separately and considered to be unrelated. It covers the necessary combinatorial and algorithmic background material; the various biological phenomena; the mathematical, population genetic, and phylogenetic models that capture the essential elements of these phenomena; the combinatorial and algorithmic problems that derive from these models; the theoretical results that have been obtained; related software that has been developed; and some empirical testing of the software on simulated and real biological data.
Cover......Page 1
Contents......Page 8
Preface......Page 12
Acknowledgments......Page 20
1 Introduction......Page 22
2 Trees First......Page 56
3 A Deeper Introduction to Recombination and Networks......Page 82
4 Exploiting Recombination......Page 118
5 First Bounds......Page 148
6 Fundamental Combinatorial Structure and Tools......Page 198
7 First Uses of Fundamental Structure......Page 218
8 Galled Trees......Page 256
9 General ARG Construction Methods......Page 306
10 The History and Forest Lower Bounds......Page 382
11 Conditions to Guarantee a Fully Decompose dMinARG......Page 402
12 Tree and ARG-Based Haplotyping......Page 410
13 Tree and ARG-Based Association Mapping......Page 454
14 Extensions and Connections......Page 490
Appendix AA Short Introduction to Integer Linear Programming......Page 544
Bibliography......Page 554
Index......Page 586
Science
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<P>In this book, Dan Gusfield examines combinatorial algorithms to construct genealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs). The algorithms produce networks (or information about networks) that serve as
The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an i
From the reviews of the previous editions ".... The book is a first class textbook and seems to be indispensable for everybody who has to teach combinatorial optimization. It is very helpful for students, teachers, and researchers in this area. The author finds a striking synthesis of nice and inte
<P>From the reviews of the first edition:</P><P>".... The book is a first class textbook and seems to be indispensable for everybody who has to teach combinatorial optimization. It is very helpful for students, teachers, and researchers in this area. The author finds a striking synthesis of nice and