Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

Molecules: Proteins and RNA

Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example
Gene3D and Understanding Proteome Evolution
The Evolution of the Globins: We Thought We Understood It
The Structurally Constrained Neutral Model of Protein Evolution
Towards Unifying Protein Evolution Theory
Molecules: Genomes
A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering
Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life
Phylogenetic Analysis
Molecular Phylogenetics: Mathematical Framework and Unsolved Problems
Phylogenetics and Computational Biology of Multigene Families
SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis
Networks
Evolutionary Genomics of Gene Expression
From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation
Populations
Drift and Selection in Evolving Interacting Systems
Adaptation in Simple and Complex Fitness Landscapes
Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity.