Alternative models to the theory of universal common descent have, thus far, been underdeveloped. Our previous work introduced a dependency graph model as an alternative way of explaining the patterns of genetic similarity and diversity among living things. According to this model, different forms of life share similarities because they share function-specific genetic features (modules) that may have dependencies on other genetic features. Here, we introduce a tool (AminoGraph) that infers dependency graphs from protein sequence alignments, and we apply this to prestin, a mammalian auditory protein that requires special modifications for ultrasonic hearing in species that use echolocation. Prestin sequences from some echolocating bats show similarities with prestin sequences from echolocating whales. Conventional analyses interpret this as convergence, not because convergence is known to be evolutionarily feasible, but because this preserves the presumed phylogenetic tree. The AminoGraph analysis of prestin presented here provides an alternative explanation: echolocation is supported by two prestin-modifying modules, one or both of which are seen in all echolocating bats and whales. The reliability of this inference is increased by thorough testing of AminoGraph on generated test data sets where sequences are either unrelated, related by common descent, or related by deployment of modules. In all cases, AminoGraph produces the expected relationships.