Phytochrome photoreceptors regulate almost all aspects of plant development, including agronomically important processes such as flowering time, fruit maturation, and shade avoidance. Gene duplication and divergence have produced a phytochrome family with two key players, phyA and phyB. They occur in all sampled seed plants and they function complementarily and antagonistically in open and shaded habitats to promote development in all terrestrial ecosystems. Episodes of positive selection and radical amino acid replacement mark several branches in the phytochrome phylogeny, concentrated in the phyA lineage. We hypothesize that amino acid residues at the affected sites are candidate determinants of phyA and phyB specificity and we are testing this using site-directed mutagenesis. Other projects in the lab use data from phytochrome genes to infer organismal phylogenies, sometimes yielding trees that conflict with those from using phylogenomic approaches. It is not clear that this results simply from biases in single gene results.