Over the phone one day in the lab, Jones told Masly what his analysis turned up.
"You're not going to believe this, but you're right," said Jones. "It's not on the fourth chromosome. It's on the third."
"That was really exciting," says Masly. "It was completely unexpected and it made the cause of this hybrid's sterility very simple; the gene's on number four in one species and on number three in the other, so when you mate the two, every now and then you'll get a male with a combination that includes no gene at all. These guys are sterile because they completely lack a gene that's necessary for fertility."
The gene, called JYAlpha, is one of the same genes that is essential for sperm motility in the flies, as well as in humans and other mammals.
Masly's work shows a back door through which speciation can start. If the right genes jump around in the genome, a population can begin creating individuals that can't successfully mate with the general population. If other speciation pressures, like geographic isolation, are added to the mix, the pressure may be enough to split one species into two new species.
When asked if JYAlpha may be responsible for melanogaster and simulans' initial split a few million years ago, Masly replied, "That's lost to history."
Fortunately, the theory isn't.