"So it looks like, after gene duplication, there is a division of labor," Zhang said. "Before duplication, the gene is supposed to do both jobs: digestion and degrading double-stranded RNA. After duplication, one copy seems to retain the activity of degrading double-stranded RNA while the other copy has adapted to changed pH in the small intestine so it can better digest food."
Even after clearly demonstrating parallel evolution in this case, Zhang believes the phenomenon is uncommon at the protein sequence level. However, he proposes a list of criteria in the Nature Genetics paper that he and other researchers can use to test apparent examples in the future.