Introduction. Statistical and computational challenges in molecular phylogenetics and evolution

1. INTRODUCTION Since the widespread acceptance of Darwin's theory of evolution (Darwin 1859), scientists have been interested in reconstructing the evolutionary relationships of living (and extinct) organisms. Evolution occurs too slowly to be experimented upon in situ in any but the most extreme cases, and scientists must look for information in the contemporary world that can lead to insights into the past. While perhaps the fossil record used to be the most obvious and explicit source of this information, starting from the early 1960s molecular sequences have taken over as the primary source of information on which to base reconstructions of the evolutionary history of life. The patterns of similarity and difference between the genomes of organisms related by descent from common ancestors implicitly hold vast amounts of information about species' relationships, and there is also considerable interest in describing and understanding the processes by which genomic sequences change over evolutionary time. The study of relationships of organisms and the study of the change of their genomes are intimately linked, and this has led to the forming of a coherent research community in molecular phylogenetics and evolution.