Population Genomics of Adaptive Radiation

Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high-throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole-genome scales. Here we review how population genomic data have facilitated our knowledge of adaptive radiation in five key areas: 1) phylogenetics, 2) hybridization, 3) timing and rates of diversification, 4) genomic basis of trait evolution, and 5) the role of genome structure in divergence. We review current knowledge in each area, highlight outstanding questions, and focus on methods that facilitate detection of complex patterns in population evolutionary demography. Among patterns that emerge, we particularly note that hybridization—and the hypothesized processes by which it shapes diversification—and questions seeking to bridge the divide between microevolutionary and macroevolutionary processes as rich areas for future study. Overall, access to population genomic data have facilitated an exciting era in adaptive radiation research, with implications for deeper understanding of fundamental evolutionary processes across the tree of life.