Comparative genome sequencing has allowed researchers to use phylogenies to map genotype to phenotype. Here I present three examples using such approaches, which we term PhyloG2P. First I present recent work by former postdoc Maude Baldwin showing convergence in sweet taste perception between hummingbirds and oscine passerine birds. Next we use convergent evolution to link genotype to phenotype in paleognathous birds, which include the flying tinamous of the New World and the flightless ratites (emu, ostrich, kiwi, etc), which are thought to have lost flight multiple times convergently. By examining evolutionary rates using a novel hierarchical Bayesian model, we identified a suite of conserved noncoding elements undergoing relaxation or acceleration in specific ratite lineages or convergently in multiple ratite lineages, suggesting a number of developmental and skeletal pathways undergoing evolutionary change in flightless birds. ATAC-seq and enhancer screens confirm that acceleration of these elements is associated with changes in the ability to drive gene expression in the developing forelimb. Lastly, I report identification of a color gene associated with color in an Andean tanager with a ‘leapfrog’ distribution, in which the central population differs in plumage from northern and southern populations. Together our results show that natural experiments and convergent evolution point to a strong role for non-coding regulatory evolution in the evolution of novel phenotypes in birds.