Recombinatorics ― The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks

In this book, Dan Gusfield examines combinatorial algorithms to constructgenealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs).The algorithms produce networks (or information about networks) that serve as hypotheses about thetrue genealogical history of observed biological sequences and can be applied to practicalbiological problems.

Phylogenetic trees have been the traditional means torepresent evolutionary history, but there is a growing realization that networks rather than treesare often needed, most notably for recent human history. This has led to the development of ARGs inpopulation 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 andexplicit phylogenetic networks, and algorithms to reconstruct or deduce information about thosenetworks.

ReCombinatorics, a groundbreaking contribution tothe emerging field of phylogenetic networks, connects and unifies topics in population genetics andphylogenetics that have traditionally been discussed separately and considered to be unrelated. Itcovers the necessary combinatorial and algorithmic background material; the various biologicalphenomena; the mathematical, population genetic, and phylogenetic models that capture the essentialelements of these phenomena; the combinatorial and algorithmic problems that derive from thesemodels; 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.

Dan Gusfield is Professor of Computer Science at the University of California, Davis. He is the coauthor of The Stable Marriage Problem: Structure and Algorithms (MIT Press) and author of Algorithms on Strings, Trees, and Sequences.