Phylogenetics is the New Genetics (for Most of Biodiversity)

Despite substantial progress in understanding the genetic basis for differences in morphology, physiology, and behavior, many phenotypes of interest are difficult to study with traditional genetic approaches because their origin traces to deep nodes in the tree of life. Moreover, many species are not amenable to either large-scale sampling or laboratory crosses. We argue that phylogenetic methods and theory provide tremendous power to identify the functional genetic variation underlying trait evolution. We anticipate that existing statistical comparative approaches will be more commonly applied to studying the genetic basis for phenotypic evolution as whole genomes continue to populate the tree of life. Nevertheless, new methods and approaches will be needed to fully capitalize on the power of clade-scale genomic datasets.