ective Synthetic Biology of Phenotypic Adaptation in Vertebrates: The Next Frontier

For over the last 2 decades, positively selected amino acid sites have been inferred almost exclusively by showing that the number of nonsynonymous substitutions per nonsynonymous site (dn) is greater than that of synonymous substitutions per synonymous site (ds). However, virtually none of these statistical results have been experimentally tested and remain as hypotheses. To perform such experimental tests, we must connect genotype and phenotype and relate the phenotypic changes to the environmental and behavioral changes of the organism. The genotype–phenotype relationship can be established only by synthesizing and manipulating “proper ” ancestral phenotypes, whereas the actual functions of adaptive mutations can be learned by studying their chemical roles in phenotypic changes. Key words: phenotypic adaptation, molecular adaptation, visual pigments, ancestral phenotypes. The molecular basis of phenotypic adaptation in higher eukaryotes is a central unanswered question in evolutionary biology. Using microorganisms, various evolutionary hypoth-eses have been tested experimentally, and adaptive mutations have been identified (e.g., Dean and Thornton 2007; Romero and Arnold 2009). However, for higher eukaryotes, particu