Research Signpost 37/661 (2), Fort P.O., Trivandrum-695 023, Kerala, India Dynamical Genetics, 2004: 49-78 ISBN: 81-7736-231-3 Editors: Valerio Parisi, Valeria De Fonzo and Filippo Aluffi-Pentini 3 Evolutionary analyses of genetic recombination Nicole Lewis-Rogers 1 , Keith A. Crandall 1 and David Posada 2 1 Department of Microbiology and Molecular Biology, Brigham Young University, Provo UT 84602, USA; 2 Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología Universidad de Vigo, Vigo 36200, Spain Abstract Recombination is one of the key evolutionary processes shaping the architecture of genomes. Quantifying the effect of recombination is crucial to our understanding of how genetic diversity is generated and maintained in populations, for the design and analysis of studies aimed at uncovering the genetic basis for disease, and for studying the evolution of virulence and pathogenicity in bacteria and virus. Ignoring the occurrence of recombination may influence the analysis of genetic data and the conclusions derived from it. Here we describe the evolutionary significance of recombination, its detection and estimation, and its effect on evolutionary analysis. We further characterize the significance of recombination in four biological systems: bacteria, virus, mitochondria, and the human genome. Correspondence/Reprint request: Prof. David Posada, Departamento de Bioquímica, Genética e Inmunología, Facultad de Ciencias Universidad de Vigo, Vigo 36200, Spain. E-mail: dposada@uvigo.es