Comparative genomics and the diversity of life

In the last decade, genomics has come to play a central role in systematics and biodiversity research. In coming years, systematics and phylogenetics will come to play an increasingly important role in genomics. Here, we address the false dichotomy between descriptive-and hypothesis-driven work, discuss the power of descriptive genomics to test questions of broad interest and explore the applications and challenges that arise as comparative genomic analyses come to include more species. Integrated phylogenetic analyses of genome sequences and organism phenotypes across many species will provide a powerful window on genome function that can be used to answer many questions that to date were only tractable in laboratory model systems. Many challenges will arise as the numbers of species in genomic analyses grow by orders of magnitude. In particular, our current nomenclatural systems for describing gene homology (orthology, paralogy and related terms) are breaking down, and the current focus on 'strict orthologs' in many comparative genome analyses will need to be replaced by more holistic approaches that better accommodate gene duplication and loss.