AminoGraph Analysis of the Auditory Protein Prestin From Bats and Whales Reveals a Dependency-Graph Signal That Is Missed by the Standard Convergence Model

Abstract

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