Introduction

J. A. Eisen originally coined the term phylogenomics and defined the discipline as the prediction of gene function and study of gene and genome evolution using molecular phylogenies in conjunction with modern comparative methods. Gene trees that have been inferred from deoxyribonucleic acid sequence data represent fundamental units of analysis in various types of phylogenomic studies. In contrast, when a single gene tree is used to infer a phylogeny of populations or species, as has been done innumerable times in traditional molecular phylogenetics, then the researcher is extrapolating an organismal phylogeny from a molecular phylogeny. In Tree of Life studies, an organismal phylogeny is more commonly referred to as a species tree because it shows the branching relationships and times of divergence among populations or species. The Illumina platforms have provided a substantial boost to phylogenomic studies in a number of ways. The chapter also presents an overview of the key concepts discussed in this book.