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. Genome sequencing is rapidly spreading beyond model organisms, opening the door to comparative studies that can reveal the genetic basis for phenotypic variation across species. Nevertheless, statistical comparative methods have not been frequently applied to these data.New phylogenetic methods have been developed with the explicit goal of linking genes and even specific mutations to species differences (‘PhyloG2P’). Applications of these methods show great promise for uncovering new sources of functional variation and tackling traits beyond the reach of traditional genetic approaches.Parallel advances in statistical comparative methods present new avenues for expanding the phylogenetic toolkit and creating tailored approaches for mapping genotype to phenotype.