So 2/3 of the time, we have “ de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist?” Okay. Somebody better go put their arm around the Selfish Gene. It’s tough being the Last Darwinian. Gene, we did not do this to you. Francis Collins and Craig Venter did this to you. Honest.
“We suspect that if one’s model system or species of study does something unique and interesting, TRGs [taxonomically restricted genes, aka orphans] will be at least partially responsible, and worth seeking out.” Curiously, the PNAS paper seems to show that.