Mathematics of Evolution and Phylogeny

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Why?

The present book brings together papers presented at a conference on this topic that was held at the Institut Henri Poincaré (Paris) in June 2003. More than 200 specialists attended the conference and we were obliged to turn down a number of other attendance requests. This field is currently the focus of major interest:

- Phylogenetics and sequence evolution investigations lay the foundations of comparative genomics and are thus keystones for bioinformatics and deciphering genomes.

- Phylogenetics is also the focal point of large-scale international biodiversity assessment initiatives such as the "Tree of Life" project, which was set up with the aim of building the evolutionary tree for all extant species.

- Systematic sequencing of genes and genomes for a broad range of species has generated in-depth information to enhance the reconstruction of evolutionary history.

- The powerful potential of computers is also being tapped to process ever-expanding datasets, while applying increasingly sophisticated mathematical models capable of accurately representing real evolutionary processes.

- Mathematics have close long-standing links with genetics, evolutionary studies and phylogenetics; this science is crucial to these latter fields and enhanced by interactions with them, e.g. through works on metrics, trees or Markov processes

- Computer science has similar close links with phylogenetics, and many recent algorithmic studies are based on phylogeny reconstruction issues.

The conference was also successful because of the quality of the speakers, who are foremost scientists in their specific fields. This success was further promoted by the conference format, i.e. speakers had sufficient time (75 min) to survey their research domain, outline their specialised focuses of interest and then review their most recent results. All conference participants were thus introduced to or gained further insight into new horizons, grasped the challenges, biological concepts and mathematical and computational tools, while learning about the latest advances.

The present book is a record of the outstanding state of the art reports presented by the conference speakers and provides a response to the substantial current interest in this research field. The different chapters give a detailed overview of each topic, from the underlying concepts to the latest results. It will therefore be equally useful for under- and post-graduate students, PhD candidates and confirmed scientists. Very few books provide a detailed account of mathematical and computational aspects of evolution and phylogeny (apart from the noteworthy book of Semple and Steel, OUP, 2003), and none cover the range of topics presented here—some of which are based on very recent studies and are currently at the forefront in the scientific news.

Outline

Anne BERGERON, Université du Québec, Montréal, Canada,
Julia Mixtacki, Bielefeld Universität, Germany,
Jens Stoye, Bielefeld Universität, Germany.
"The Reversal Distance Problem" (Abstract)

David BRYANT, McGill University, Montréal, Canada,
Nicolas GALTIER, CNRS-Université de Montpellier II, France,
Marie-Anne POURSAT, Université d’Orsay, France.
"Likelihood Calculation in Molecular Phylogenetics" (Abstract)

Richard DESPER, NCBI, Bethesda, USA,

Olivier GASCUEL, CNRS-Université Montpellier II, France.
"The Minimum Evolution Distance-Based Approach of Phylogenetic Inference" (Abstract)

Nadia EL-MABROUK, Université de Montréal, Canada
"Genome rearrangement with gene families" (Abstract)

Olivier GASCUEL, CNRS-Université Montpellier II, France,
Denis BERTRAND, CNRS-Université Montpellier II, France
Olivier ELEMENTO, Princeton University, USA,
"Reconstructing the duplication history of tandemly repeated sequences" (Abstract)

Mike HENDY, Massey University, New-Zealand.
"Hadamard conjugation - an analytic tool for phylogenetics" (Abstract)

Susan HOLMES, Stanford University, USA.
"Statistical Approach to Tests Involving Phylogenies" (Abstract)

David BRYANT, McGill University, Montréal, Canada,

Katharina HUBER, Uppsala University, Sweden,
Vincent MOULTON, Uppsala University, Sweden.
"Phylogenetic Networks" (Abstract)

Bernard MORET, University of New Mexico, USA,
Jijun TANG, University of New Mexico, USA,
Tandy WARNOW, University of Austin, USA.
"Reconstructing Phylogenies from Gene-Content and Gene-Order Data" (Abstract)

Elchanan MOSSEL, U.C. Berkeley, USA,

Mike STEEL, University of Canterbury, New-Zealand.
"How much can evolved characters tell us about the tree that generated them?" (Abstract)

Mark PAGEL, University of Reading, UK,
Andrew MEADE, University of Reading, UK.
"Mixture Models in Phylogenetic Inference" (Abstract)

David SANKOFF, Université d’Ottawa, Canada.
"Conserved Segment Statistics and Rearrangement Inferences in Comparative Genomics" (Abstract)

Li-San WANG, Pensylvania University, USA.
Tandy WARNOW, University of Austin, USA
"Distance-Based Genome Rearrangement Phylogeny (Abstract)

Ziheng YANG, University College London, UK.
"Bayes inference in molecular phylogenetics" (Abstract)

Scientific editor: Olivier GASCUEL

Institut Henri Poincaré Conference