27Studies of opsin genes offer insights into the evolutionary history and molecular basis of vertebrate 28 color vision, but most assume intact open reading frames equate to functional phenotypes. Despite 29 known variation in opsin repertoires and associated visual phenotypes, the genetic basis of such 30 patterns has not been examined at each step of the central dogma. By comparing sequences, gene 31 expression, and protein localization across a hyperdiverse group of mammals, noctilionoid bats, 32we find evidence that independent losses of S-opsin arose through disruptions at different stages 33 of protein synthesis, while maintenance relates to frugivory. Discordance between DNA, RNA, 34 and protein reveals that the loss of short-wave sensitivity in some lineages resulted from 35 transcriptional and post-transcriptional changes in addition to degradation of open reading frames. 36These mismatches imply that visual phenotypes cannot reliably be predicted from genotypes alone, 37 and connect ecology to multiple mechanisms behind the loss of color in vertebrates. 38 39 Introduction 40