Reconstructing Evolution New Mathematical and Computational Advances

by Gascuel, Olivier; Steel, Mike

• ISBN13: 9780199208227
• ISBN10: 0199208220
• eBook ISBN(s): 9780191525988
• Format: Hardcover
• Copyright: 2007-08-23
• Publisher: Oxford University Press

Summary

Evolution is a complex process, acting at multiple scales, from DNA sequences and proteins to populations of species. Understanding and reconstructing evolution is of major importance in numerous subfields of biology. For example, phylogenetics and sequence evolution is central to comparativegenomics, attempts to decipher genomes, and molecular epidemiology. Phylogenetics is also the focal point of large-scale international biodiversity assessment initiatives such as the 'Tree of Life' project, which aims to build the evolutionary tree for all extant species. Since the pioneering work in phylogenetics in the 1960s, models have become increasingly sophisticated to account for the inherent complexity of evolution. They rely heavily on mathematics and aim at modelling and analyzing biological phenomena such as horizontal gene transfer, heterogeneity ofmutation, and speciation and extinction processes. This book presents these recent models, their biological relevance, their mathematical basis, their properties, and the algorithms to infer them from data. A number of subfields from mathematics and computer science are involved: combinatorics,graph theory, stringology, probabilistic and Markov models, information theory, statistical inference, Monte Carlo methods, continuous and discrete algorithmics. This book arises from the em/Mathematics of Evolution and Phylogenetics/em meeting at the Mathematical Institute Henri Poincare, Paris, in June 2005 and is based on the outstanding state-of-the-art reports presented by the conference speakers. Ten chapters - based around five themes - provide adetailed overview of key topics, from the underlying concepts to the latest results, some of which are at the forefront of current research.

Author Biography

Olivier Gascuel leads a research group at LIRMM-CNRS, Montpellier. He is an associate editor of Systematic Biology and belongs to the editorial board of BMC-Bioinformatics, BMC-Evolutionary Biology, and BMC-Algorithms for Molecular Biology. He has published 110 papers and book chapters, and authored several widely used programs in phylogenetics and bioinformatics. Mike Steel directs the Biomathematics Research Centre at the University of Canterbury, New Zealand and is an associate editor of the journal Systematic Biology. He has published 120 papers and book chapters on mathematical aspects of evolutionary biology, and is co-author of the book Phylogenetics (Oxford University Press, 2003).

Table of Contents

Introduction

List of Contributors

I Evolution in populations

Trees of genes in populations

The evolutionary analysis of measurably evolving populations using serially sampled gene sequences

Models of sequence evolution

Modelling the variability of evolutionary processes

Phylogenetic invariants

Tree shape, speciation and extinction

Some models of phylogenetic tree shape

Phylogenetic diversity: from combinatorics to ecology

Trees from subtrees and characters

Fragmentation of large data sets in phylogenetic analyses

Identifying and defining trees

From trees to networks

Split networks and reticulate networks

Hybridization networks

Index

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