The near universality of the genetic code is frequently cited as evidence for universal common ancestry. On the other hand, critics of universal common ancestry frequently point to exceptions to the universal code as evidence against it. However, there has never been a comprehensive investigation into the character and distribution of variant genetic codes and their implications for the debate over universal common ancestry. This paper develops a framework for understanding codes within a common design framework, based crucially on the premise that some genetic code variants are designed and others are the result of mutations to translation machinery. We found that these two sources of variant codes can be distinguished by considering organismal lifestyle, taxonomic rank, evolutionary feasibility, codon rarity and complexity of distribution. These different approaches to distinguishing the codes give highly correlated results, demonstrating impressive explanatory power for our framework. In contrast, we find that evolutionary theory has difficulty explaining the character and distribution of variant genetic codes.

Supplemental files: Table of Nuclear Codes, Table of Mitochondrial Codes