Evolutionary Processes That Shape Genomic and Phenotypic Variation
The availability of genomic data from a remarkable range of species has allowed the alignment and comparison of whole genomes. These comparative approaches have been used to characterize the relative importance of fundamental evolutionary processes that cause genomic evolution and to identify particular regions of the genome that have experienced recent positive selection, recurrent adaptive evolution, or extreme sequence conservation–. Yet more recently, resequencing of additional individuals or populations is also allowing genome-wide population genetic analyses within species –. Such population-level comparisons will allow even more powerful study of the relative importance of particular evolutionary processes in molecular evolution as well as the identification of candidate genomic regions that are responsible for key evolutionary changes (e.g., sticklebacks , butterflies , Arabidopsis ). These data, combined with theoretical advances, should provide insight into long-standing questions such as the prevalence of balancing selection, the relative frequency of strong versus weak directional selection, the role of hybridization, and the importance of genetic drift. A key challenge will be to move beyond documenting the action of natural selection on the genome to understanding the importance of particular selective agents. For example, what proportion of selection on genomes results from adaptation to the abiotic environment, coevolution of species, sexual selection, or genetic conflict? Finally, as sequencing costs continue to drop and analytical tools improve, these same approaches may be applied to organisms that present intriguing evolutionary questions but were not tractable methodologically just a few years ago. The nonmodel systems of today may well become the model systems of tomorrow .
Understanding Biological Diversification
A major and urgent challenge is to improve knowledge of the identity and distribution of species globally. While we need to retain the traditional focus on phenotypes, powerful new capabilities to obtain and interpret both genomic and spatial data can and should revolutionize the science of biodiversity. Building on momentum from single-locus “barcoding" efforts, new genome-level data can build bridges from population biology to systematics . By establishing a comprehensive and robust “Tree of Life," we will improve understanding of both the distribution of diversity and the nature and timing of the evolutionary processes that have shaped it.