Abstract
Population genomic tools have revolutionized many aspects of biology, as detailed throughout the chapters of this volume. In particular, population genomics has provided key insights into ecological and evolutionary processes in natural and managed populations. These studies address a wide range of questions, including demography, phylogeny, genetics of ecologically relevant traits, and adaptation. They have also facilitated the conservation and management of biodiversity and harvested populations. Rather than exhaustively document the applications of population genomics in ecology and evolution, in this chapter we provide perspectives on a few key issues confronting researchers seeking to use population genomic tools in non-model systems. A wide variety of molecular and computational genomic approaches are available and have been used in ecological and evolutionary studies. There is no single best approach; rather, the genomic approach used should be tailored to best address the particular study goals and guided by the biology of the system. A large number of trade-offs, costs, and benefits distinguish genomic approaches, which we discuss below. To illustrate these issues, we focus on several published case studies and assess how the research questions were addressed.