Studying Natural Selection in the Era of Ubiquitous Genomes

A major goal of comparative genomics research is modeling changes in DNA sequences between species to understand the evolutionary forces acting on species differences. Application of these models to a number of species over the past decade has revealed some commonalities across organisms, most notably a consistent role of positive selection in shaping the molecular evolution of the immune system. However, models of DNA sequence evolution also have important limitations that are increasingly being recognized, including issues with data quality and biases caused by simplifying assumptions. While new approaches have begun to address these challenges, ultimately, additional data, such as resequencing data from populations, will provide more power to fully understand the unique evolutionary forces acting on different species. In this review, I summarize the conclusions of recent genome-wide studies of selection, highlight some important challenges to applying these methods to large data sets, and discuss ways forward for the field.